Worked Example: PCA on SNPs data from a vcf file Part 1 - Data Preparation
Gabriel Medeiros
2022-11-19
Introduction
In this worked example you will replicate a PCA on a published dataset.
The example is split into 2 Parts:
- Part 1: Data Preparation (this file)
- Part 2: Data analysis with PCA
In this Data Preparation phase, you will do the following things:
- Load the SNP genotypes in .vcf format
(
vcfR::read.vcfR()) - Extract the genotypes into an R-compatible format
(
vcfR::extract.gt()) - Rotate the data into the standard R analysis format
(
t()) - Remove individuals (rows) from the data set that have >50% NAs (using a function I wrote)
- Remove SNPs (columns) that are fixed
- Impute remaining NAs (using a
for()loop) - Save the prepared data as a
.csvfile for the next step (write.csv())
Biological background
This worked example is based on a paper in the journal Molecular Ecology from 2017 by Jennifer Walsh titled Subspecies delineation amid phenotypic, geographic and genetic discordance in a songbird.
The study investigated variation between two bird species in the genus Ammodramus: A. nenlsoni and A. caudacutus.
The species A. nenlsoni has been divided into 3 sub-species: A. n. nenlsoni, A.n. alterus, and A n. subvirgatus. The other species, A. caudacutus, has been divided into two subspecies, A.c. caudacutus and A.c. diversus.
The purpose of this study was to investigate to what extent these five subspecies recognized by taxonomists are supported by genetic data. The author’s collected DNA from 75 birds (15 per subspecies) and genotyped 1929 SNPs. They then analyzed the data with Principal Components Analysis (PCA), among other genetic analyzes.
This tutorial will work through all of the steps necessary to re-analyze Walsh et al.s data
Tasks
In the code below all code is provided. Your tasks will be to do 2 things:
- Give a meaningful title to all sections marked “TODO: TITLE”
- Write 1 to 2 sentences describing what is being done and why in all sections marked “TODO: EXPLAIN”
Preliminaries
Load the vcfR and other packages with library().
library(vcfR) ## Warning: package 'vcfR' was built under R version 4.2.2##
## ***** *** vcfR *** *****
## This is vcfR 1.13.0
## browseVignettes('vcfR') # Documentation
## citation('vcfR') # Citation
## ***** ***** ***** *****library(vegan)## Warning: package 'vegan' was built under R version 4.2.2## Loading required package: permute## Warning: package 'permute' was built under R version 4.2.2## Loading required package: lattice## This is vegan 2.6-4library(ggplot2)
library(ggpubr)Make sure that your working directory is set to the location of the
file all_loci.vcf.
getwd()## [1] "C:/Users/Grief Mage/Documents"list.files()## [1] "07-mean_imputation---Gabriel-Medeiros.html"
## [2] "07-mean_imputation--1-.docx"
## [3] "07-mean_imputation--1-.html"
## [4] "09-PCA_worked_example-SNPs-part1.Rmd"
## [5] "1000-genomes"
## [6] "all_loci.vcf"
## [7] "bird_snps_remove_NAs.Rmd"
## [8] "cover letter.pdf"
## [9] "desktop.ini"
## [10] "Dolphin Emulator"
## [11] "FPSMonitor.txt"
## [12] "GitHub"
## [13] "gpm23_Lab9"
## [14] "IEF essay 2.txt"
## [15] "League of Legends"
## [16] "My Games"
## [17] "My Music"
## [18] "My Pictures"
## [19] "My Videos"
## [20] "my_snps"
## [21] "NetBeansProjects"
## [22] "R files"
## [23] "removing_fixed_alleles.html"
## [24] "removing_fixed_alleles.Rmd"
## [25] "rsconnect"
## [26] "SNPs_cleaned.csv"
## [27] "transpose_VCF_data.html"
## [28] "transpose_VCF_data.Rmd"
## [29] "vcfR_test.vcf"
## [30] "vcfR_test.vcf.gz"
## [31] "walsh2017morphology.csv"
## [32] "working_directory_practice.html"
## [33] "working_directory_practice.Rmd"
## [34] "Zoom"list.files(pattern = "vcf")## [1] "all_loci.vcf" "vcfR_test.vcf" "vcfR_test.vcf.gz"Data preparation
Loading .vcf file
The function read.vcfR is loading the “all_loci.vcf” file in the working directory. It is taking the SNP data from the file and loading it into a variable called “snps”
snps <- vcfR::read.vcfR("all_loci.vcf", convertNA = TRUE)## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 1929
## column count: 81
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 1929
## Character matrix gt cols: 81
## skip: 0
## nrows: 1929
## row_num: 0
##
Processed variant 1000
Processed variant: 1929
## All variants processedTODO: Extracting numeric values
The function “vcfR::extract.gt()” converts our SNPs into a numeric value that can be used for analysis processes like PCA.
snps_num <- vcfR::extract.gt(snps,
element = "GT",
IDtoRowNames = F,
as.numeric = T,
convertNA = T,
return.alleles = F)TODO: Flipping the values
The “t()” allows us to flip the matrix so the SNP numeric values are in the columns and not in the rows.
snps_num_t <- t(snps_num) We convert the matrix to a data frame type using “data.frame()”.
snps_num_df <- data.frame(snps_num_t) TODO: Locating NA values
This function “find_NAs” traverses through the matrix and finds the amount of NA’s there are as well as where those NA’s are located in the matrix.
find_NAs <- function(x){
NAs_TF <- is.na(x)
i_NA <- which(NAs_TF == TRUE)
N_NA <- length(i_NA)
cat("Results:",N_NA, "NAs present\n.")
return(i_NA)
}
find_NAs(snps_num_df)## Results: 15843 NAs present
## .## [1] 31 36 37 39 41 43 45 50 52 53
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## [2371] 23441 23443 23452 23453 23454 23461 23468 23503 23508 23509
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## [5271] 50071 50076 50077 50078 50079 50081 50083 50085 50086 50090
## [5281] 50093 50096 50151 50164 50165 50223 50236 50237 50287 50288
## [5291] 50293 50294 50295 50297 50299 50306 50308 50309 50359 50365
## [5301] 50367 50369 50371 50380 50381 50398 50431 50432 50439 50453
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## [10571] 92703 92711 92717 92724 92726 92731 92733 92735 92736 92771
## [10581] 92773 92774 92775 92777 92789 92839 92840 92845 92846 92847
## [10591] 92849 92851 92861 92911 92912 92915 92916 92919 92921 92923
## [10601] 92929 92930 92932 92933 92983 92988 92989 92991 92993 92995
## [10611] 93002 93005 93054 93055 93061 93063 93065 93069 93076 93077
## [10621] 93082 93087 93088 93092 93093 93094 93135 93149 93205 93206
## [10631] 93207 93209 93211 93218 93221 93224 93277 93278 93279 93281
## [10641] 93283 93290 93293 93296 93343 93344 93351 93353 93355 93362
## [10651] 93364 93365 93415 93420 93421 93423 93425 93427 93434 93436
## [10661] 93437 93448 93454 93487 93492 93493 93495 93497 93499 93506
## [10671] 93508 93509 93520 93526 93559 93564 93565 93567 93569 93571
## [10681] 93578 93580 93581 93592 93598 93631 93639 93641 93653 93711
## [10691] 93725 93775 93776 93780 93781 93783 93785 93797 93855 93861
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## [10711] 93941 93949 93956 93957 93997 93999 94001 94013 94068 94069
## [10721] 94071 94085 94135 94136 94141 94142 94143 94145 94147 94150
## [10731] 94153 94156 94157 94158 94161 94207 94208 94213 94214 94215
## [10741] 94217 94219 94222 94225 94228 94229 94230 94233 94285 94287
## [10751] 94289 94291 94293 94300 94301 94303 94318 94351 94357 94359
## [10761] 94361 94363 94365 94373 94379 94389 94390 94423 94424 94429
## [10771] 94430 94431 94433 94434 94445 94499 94501 94502 94503 94505
## [10781] 94507 94509 94517 94518 94520 94523 94532 94534 94567 94568
## [10791] 94573 94574 94575 94577 94579 94589 94604 94639 94647 94649
## [10801] 94653 94660 94661 94663 94711 94716 94718 94719 94721 94733
## [10811] 94774 94791 94805 94846 94863 94877 94935 94949 94999 95000
## [10821] 95004 95005 95007 95009 95011 95020 95021 95024 95071 95072
## [10831] 95076 95077 95079 95081 95083 95092 95093 95096 95143 95151
## [10841] 95153 95165 95180 95215 95220 95222 95223 95225 95237 95252
## [10851] 95287 95292 95294 95295 95297 95309 95324 95359 95360 95364
## [10861] 95365 95367 95369 95381 95431 95432 95436 95437 95439 95441
## [10871] 95453 95503 95504 95509 95510 95511 95513 95515 95517 95525
## [10881] 95530 95531 95533 95536 95540 95541 95542 95579 95581 95582
## [10891] 95583 95585 95587 95594 95597 95598 95612 95651 95653 95654
## [10901] 95655 95657 95659 95666 95669 95670 95684 95727 95741 95799
## [10911] 95813 95863 95869 95871 95885 95906 95908 95915 95941 95943
## [10921] 95945 95957 95985 96013 96014 96015 96017 96019 96021 96022
## [10931] 96026 96028 96029 96037 96041 96045 96046 96047 96057 96085
## [10941] 96086 96087 96089 96091 96093 96094 96098 96100 96101 96109
## [10951] 96113 96117 96118 96119 96129 96157 96158 96159 96161 96163
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## [10971] 96201 96229 96230 96231 96233 96235 96237 96238 96242 96244
## [10981] 96245 96253 96257 96261 96262 96263 96301 96303 96317 96354
## [10991] 96379 96380 96381 96389 96392 96395 96396 96397 96398 96403
## [11001] 96407 96444 96447 96449 96457 96461 96519 96530 96532 96533
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## [11081] 97324 97325 97336 97340 97381 97383 97385 97387 97389 97397
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## [11221] 98329 98332 98333 98336 98383 98384 98387 98389 98391 98393
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## [11271] 98614 98618 98621 98624 98626 98627 98629 98636 98671 98677
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## [11661] 102564 102565 102567 102569 102571 102581 102639 102645 102653 102654
## [11671] 102655 102656 102657 102659 102660 102661 102663 102666 102670 102672
## [11681] 102703 102709 102711 102713 102715 102725 102733 102735 102736 102775
## [11691] 102781 102782 102783 102785 102788 102789 102797 102847 102853 102854
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## [11731] 103221 103226 103228 103229 103283 103287 103301 103351 103357 103359
## [11741] 103361 103373 103423 103429 103431 103433 103435 103443 103444 103445
## [11751] 103495 103501 103503 103505 103507 103515 103516 103517 103567 103568
## [11761] 103573 103575 103581 103586 103588 103589 103604 103639 103645 103647
## [11771] 103649 103651 103652 103653 103661 103711 103712 103719 103732 103733
## [11781] 103783 103784 103791 103804 103805 103855 103856 103863 103876 103877
## [11791] 103927 103928 103932 103933 103935 103937 103948 103949 104005 104007
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## [11811] 104071 104076 104077 104078 104079 104081 104083 104093 104116 104118
## [11821] 104124 104127 104141 104143 104148 104149 104150 104151 104153 104155
## [11831] 104165 104215 104221 104222 104223 104225 104230 104234 104236 104237
## [11841] 104254 104287 104293 104294 104295 104297 104302 104306 104308 104309
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## [11861] 104581 104582 104583 104585 104587 104589 104597 104653 104654 104655
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## [11971] 105540 105550 105604 105612 105615 105616 105618 105622 105624 105661
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## [12081] 106742 106743 106745 106753 106754 106756 106757 106760 106761 106763
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## [12111] 106844 106846 106847 106848 106887 106889 106897 106901 106916 106957
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## [12151] 107483 107484 107485 107493 107535 107539 107541 107549 107555 107556
## [12161] 107557 107565 107607 107621 107679 107693 107744 107747 107749 107751
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## [12181] 107834 107837 107840 107887 107891 107893 107895 107897 107899 107900
## [12191] 107906 107909 107912 107959 107963 107965 107967 107969 107971 107972
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## [12451] 110059 110066 110068 110069 110127 110136 110137 110144 110145 110148
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## [12781] 111205 111206 111207 111209 111211 111213 111218 111221 111229 111248
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## [12871] 112213 112215 112217 112229 112279 112280 112285 112287 112289 112301
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## [12901] 112567 112575 112589 112639 112645 112646 112647 112649 112651 112660
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## [13041] 114170 114172 114173 114223 114228 114229 114230 114231 114233 114235
## [13051] 114237 114238 114242 114244 114245 114295 114296 114301 114302 114303
## [13061] 114305 114307 114309 114314 114316 114317 114325 114327 114328 114330
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## [13081] 114392 114397 114443 114445 114446 114447 114449 114451 114453 114461
## [13091] 114464 114469 114515 114517 114518 114519 114521 114523 114525 114533
## [13101] 114536 114541 114583 114591 114593 114604 114661 114663 114676 114677
## [13111] 114694 114733 114735 114748 114749 114766 114807 114821 114844 114850
## [13121] 114855 114871 114872 114873 114879 114881 114883 114893 114903 114948
## [13131] 114950 114951 114965 115020 115022 115023 115037 115092 115094 115095
## [13141] 115109 115159 115160 115165 115166 115167 115169 115171 115180 115181
## [13151] 115196 115231 115232 115237 115238 115239 115241 115243 115252 115253
## [13161] 115268 115303 115304 115309 115310 115311 115313 115315 115324 115325
## [13171] 115340 115375 115379 115380 115381 115383 115385 115387 115394 115396
## [13181] 115397 115398 115402 115405 115412 115447 115451 115452 115453 115455
## [13191] 115457 115459 115466 115468 115469 115470 115474 115477 115484 115519
## [13201] 115520 115525 115526 115527 115529 115532 115533 115540 115541 115549
## [13211] 115551 115552 115554 115556 115557 115558 115591 115596 115597 115599
## [13221] 115601 115603 115612 115613 115663 115664 115669 115670 115671 115673
## [13231] 115682 115684 115685 115735 115736 115741 115742 115743 115745 115754
## [13241] 115756 115757 115813 115814 115815 115817 115819 115820 115829 115885
## [13251] 115887 115901 115957 115959 115973 116023 116029 116031 116033 116035
## [13261] 116045 116095 116101 116103 116105 116107 116117 116167 116168 116171
## [13271] 116172 116173 116175 116177 116185 116188 116189 116245 116247 116249
## [13281] 116261 116311 116315 116317 116319 116329 116332 116333 116336 116342
## [13291] 116383 116387 116389 116391 116401 116404 116405 116408 116414 116455
## [13301] 116461 116462 116463 116465 116477 116527 116531 116532 116533 116535
## [13311] 116537 116539 116548 116549 116605 116607 116621 116677 116679 116693
## [13321] 116743 116748 116749 116750 116751 116753 116755 116765 116815 116820
## [13331] 116821 116822 116823 116825 116827 116837 116895 116909 116959 116964
## [13341] 116965 116966 116967 116969 116974 116978 116980 116981 116986 116988
## [13351] 116989 116996 116997 116998 116999 117031 117039 117041 117053 117109
## [13361] 117111 117125 117175 117181 117183 117185 117187 117196 117197 117212
## [13371] 117213 117214 117247 117253 117255 117257 117265 117269 117323 117325
## [13381] 117326 117327 117329 117331 117333 117341 117344 117357 117399 117413
## [13391] 117471 117485 117543 117557 117607 117613 117614 117615 117617 117619
## [13401] 117621 117626 117629 117632 117634 117635 117637 117644 117645 117646
## [13411] 117687 117701 117751 117756 117757 117758 117759 117761 117763 117765
## [13421] 117770 117773 117776 117781 117823 117828 117829 117830 117831 117833
## [13431] 117835 117837 117842 117845 117848 117853 117895 117901 117903 117905
## [13441] 117907 117910 117916 117917 117924 117934 117967 117968 117972 117973
## [13451] 117975 117977 117979 117988 117989 118047 118051 118061 118111 118116
## [13461] 118117 118119 118121 118123 118132 118133 118183 118184 118187 118189
## [13471] 118191 118205 118255 118256 118259 118261 118263 118277 118327 118328
## [13481] 118331 118333 118335 118349 118405 118407 118409 118411 118421 118437
## [13491] 118471 118479 118490 118493 118543 118551 118562 118565 118623 118637
## [13501] 118695 118709 118759 118764 118765 118767 118769 118771 118780 118781
## [13511] 118789 118796 118837 118839 118841 118852 118853 118897 118902 118905
## [13521] 118913 118924 118925 118933 118969 118977 118985 118996 118997 119005
## [13531] 119047 119052 119053 119055 119059 119068 119069 119119 119124 119125
## [13541] 119127 119131 119140 119141 119197 119199 119201 119203 119206 119213
## [13551] 119271 119277 119285 119288 119343 119349 119357 119360 119415 119421
## [13561] 119429 119432 119487 119493 119501 119504 119559 119565 119573 119576
## [13571] 119624 119628 119630 119631 119633 119635 119636 119644 119645 119701
## [13581] 119707 119717 119735 119767 119768 119771 119772 119775 119777 119779
## [13591] 119789 119847 119849 119860 119861 119911 119919 119921 119932 119933
## [13601] 119983 119991 119993 120004 120005 120059 120061 120062 120063 120065
## [13611] 120067 120077 120080 120135 120149 120204 120205 120207 120209 120211
## [13621] 120221 120276 120277 120279 120281 120283 120293 120343 120344 120349
## [13631] 120351 120353 120355 120364 120365 120415 120416 120421 120423 120425
## [13641] 120427 120436 120437 120476 120479 120487 120493 120494 120495 120532
## [13651] 120541 120542 120545 120555 120559 120565 120566 120567 120569 120571
## [13661] 120578 120581 120584 120631 120636 120637 120638 120639 120641 120643
## [13671] 120645 120650 120653 120709 120711 120725 120728 120781 120783 120797
## [13681] 120800 120855 120868 120869 120927 120940 120941 120968 120991 120997
## [13691] 120999 121013 121069 121070 121071 121073 121082 121084 121085 121141
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## [13731] 121429 121431 121435 121445 121462 121495 121496 121500 121501 121503
## [13741] 121505 121507 121509 121516 121517 121532 121534 121567 121572 121573
## [13751] 121575 121577 121581 121589 121604 121639 121644 121645 121647 121649
## [13761] 121653 121661 121676 121711 121716 121717 121719 121721 121723 121725
## [13771] 121733 121749 121791 121805 121855 121860 121861 121862 121863 121865
## [13781] 121867 121869 121877 121885 121892 121927 121932 121933 121934 121935
## [13791] 121937 121939 121941 121949 121957 121964 121999 122000 122005 122007
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## [13841] 122453 122503 122507 122509 122510 122511 122513 122517 122525 122583
## [13851] 122597 122655 122669 122720 122725 122727 122729 122731 122741 122792
## [13861] 122797 122799 122801 122803 122813 122863 122871 122873 122875 122885
## [13871] 122935 122942 122943 122945 122947 122954 122956 122957 122958 122963
## [13881] 122964 122968 122970 122972 122974 123007 123012 123014 123015 123019
## [13891] 123021 123024 123026 123028 123029 123033 123037 123040 123044 123045
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## [13971] 123763 123807 123809 123821 123879 123881 123893 123951 123965 124015
## [13981] 124019 124021 124022 124023 124025 124027 124030 124033 124034 124036
## [13991] 124037 124054 124087 124091 124094 124095 124100 124109 124160 124165
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## [14011] 124309 124311 124313 124324 124325 124375 124376 124379 124381 124383
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## [14031] 124524 124525 124527 124530 124541 124542 124592 124596 124597 124599
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## [14051] 124741 124743 124745 124757 124813 124815 124817 124829 124879 124885
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## [14111] 125467 125477 125527 125528 125533 125535 125545 125546 125548 125549
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## [14271] 126790 126824 126827 126828 126829 126831 126833 126845 126901 126903
## [14281] 126917 126967 126968 126971 126973 126974 126975 126979 126989 127039
## [14291] 127040 127043 127045 127046 127047 127051 127061 127111 127112 127115
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## [14331] 127333 127335 127337 127342 127345 127348 127349 127364 127399 127405
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## [14351] 127551 127565 127587 127590 127591 127596 127604 127605 127618 127619
## [14361] 127621 127622 127623 127624 127630 127636 127637 127652 127653 127654
## [14371] 127687 127692 127693 127694 127695 127697 127705 127706 127708 127709
## [14381] 127724 127759 127764 127765 127766 127767 127769 127777 127778 127780
## [14391] 127781 127796 127837 127838 127839 127841 127843 127845 127853 127856
## [14401] 127861 127911 127925 127983 127997 128052 128053 128054 128055 128057
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## [14451] 128411 128413 128414 128415 128417 128426 128428 128429 128432 128487
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## [14481] 128771 128774 128775 128777 128789 128839 128844 128845 128847 128849
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## [14751] 131341 131347 131349 131351 131361 131363 131365 131366 131367 131371
## [14761] 131374 131380 131381 131384 131395 131396 131413 131419 131421 131423
## [14771] 131433 131435 131437 131438 131439 131443 131446 131452 131453 131456
## [14781] 131467 131468 131485 131491 131493 131495 131505 131507 131509 131510
## [14791] 131511 131515 131518 131524 131525 131528 131539 131540 131557 131563
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## [14841] 131734 131740 131741 131744 131755 131756 131773 131779 131781 131783
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## [14861] 131827 131828 131845 131851 131853 131855 131865 131867 131869 131870
## [14871] 131871 131875 131878 131879 131884 131885 131888 131899 131900 131935
## [14881] 131941 131943 131945 131957 132013 132014 132015 132029 132085 132087
## [14891] 132101 132157 132159 132173 132229 132231 132245 132303 132317 132375
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## [14971] 133232 133237 133239 133241 133243 133250 133253 133303 133307 133309
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## [15151] 134629 134677 134678 134679 134681 134685 134690 134692 134693 134701
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## [15651] 138381 138384 138387 138389 138390 138392 138393 138394 138400 138403
## [15661] 138404 138406 138409 138413 138415 138418 138422 138423 138424 138425
## [15671] 138427 138430 138431 138435 138444 138447 138450 138451 138453 138456
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## [15691] 138492 138493 138495 138497 138499 138501 138509 138510 138529 138531
## [15701] 138534 138537 138543 138544 138546 138550 138551 138553 138554 138556
## [15711] 138560 138561 138565 138567 138568 138570 138577 138580 138581 138582
## [15721] 138583 138588 138591 138592 138594 138596 138598 138601 138603 138606
## [15731] 138609 138615 138616 138618 138622 138623 138625 138626 138628 138632
## [15741] 138633 138637 138639 138640 138642 138649 138652 138653 138654 138655
## [15751] 138660 138663 138664 138666 138668 138670 138673 138675 138678 138681
## [15761] 138687 138688 138690 138694 138695 138697 138698 138700 138704 138705
## [15771] 138709 138711 138712 138714 138721 138724 138725 138726 138727 138732
## [15781] 138735 138736 138738 138740 138742 138745 138747 138750 138753 138759
## [15791] 138760 138762 138766 138767 138769 138770 138772 138776 138777 138781
## [15801] 138783 138784 138786 138793 138796 138797 138798 138799 138804 138807
## [15811] 138808 138810 138812 138814 138817 138819 138822 138825 138831 138832
## [15821] 138834 138838 138839 138841 138842 138844 138848 138849 138853 138855
## [15831] 138856 138858 138865 138868 138869 138870 138871 138876 138879 138880
## [15841] 138882 138884 138886Puts the number of rows and the number of columns in there own variables. The “for” loop traverses through the rows to locate SNPs where length is. For each time through the loop, it finds the location of NAs in each row, how many there are and saves it to a vector.
# N_rows
# number of rows (individuals)
N_rows <- nrow(snps_num_t)
# N_NA
# vector to hold output (number of NAs)
N_NA <- rep(x = 0, times = N_rows)
# N_SNPs
# total number of columns (SNPs)
N_SNPs <- ncol(snps_num_t)
# the for() loop
for(i in 1:N_rows){
# for each row, find the location of
## NAs with snps_num_t()
i_NA <- find_NAs(snps_num_t[i,])
# then determine how many NAs
## with length()
N_NA_i <- length(i_NA)
# then save the output to
## our storage vector
N_NA[i] <- N_NA_i
}## Results: 28 NAs present
## .Results: 20 NAs present
## .Results: 28 NAs present
## .Results: 24 NAs present
## .Results: 23 NAs present
## .Results: 63 NAs present
## .Results: 51 NAs present
## .Results: 38 NAs present
## .Results: 34 NAs present
## .Results: 24 NAs present
## .Results: 48 NAs present
## .Results: 21 NAs present
## .Results: 42 NAs present
## .Results: 78 NAs present
## .Results: 45 NAs present
## .Results: 21 NAs present
## .Results: 42 NAs present
## .Results: 34 NAs present
## .Results: 66 NAs present
## .Results: 54 NAs present
## .Results: 59 NAs present
## .Results: 52 NAs present
## .Results: 47 NAs present
## .Results: 31 NAs present
## .Results: 63 NAs present
## .Results: 40 NAs present
## .Results: 40 NAs present
## .Results: 22 NAs present
## .Results: 60 NAs present
## .Results: 48 NAs present
## .Results: 961 NAs present
## .Results: 478 NAs present
## .Results: 59 NAs present
## .Results: 26 NAs present
## .Results: 285 NAs present
## .Results: 409 NAs present
## .Results: 1140 NAs present
## .Results: 600 NAs present
## .Results: 1905 NAs present
## .Results: 25 NAs present
## .Results: 1247 NAs present
## .Results: 23 NAs present
## .Results: 750 NAs present
## .Results: 179 NAs present
## .Results: 433 NAs present
## .Results: 123 NAs present
## .Results: 65 NAs present
## .Results: 49 NAs present
## .Results: 192 NAs present
## .Results: 433 NAs present
## .Results: 66 NAs present
## .Results: 597 NAs present
## .Results: 1891 NAs present
## .Results: 207 NAs present
## .Results: 41 NAs present
## .Results: 268 NAs present
## .Results: 43 NAs present
## .Results: 110 NAs present
## .Results: 130 NAs present
## .Results: 90 NAs present
## .Results: 271 NAs present
## .Results: 92 NAs present
## .Results: 103 NAs present
## .Results: 175 NAs present
## .Results: 31 NAs present
## .Results: 66 NAs present
## .Results: 64 NAs present
## .Results: 400 NAs present
## .Results: 192 NAs present
## .Results: 251 NAs present
## .Results: 69 NAs present
## .Results: 58 NAs present
## .Any row that has greater then 50% NAs is not being used. When the histogram below is being made, the abline will show a vertical line at the “cutoff50” point to show that anything to the right of it is not going to be used.
# 50% of N_SNPs
cutoff50 <- N_SNPs*0.5
hist(N_NA)
abline(v = cutoff50,
col = 2,
lwd = 2,
lty = 2)
We can get the percentage by dividing the number of NAs by the number SNPs and multiplying by 100. We then call “which()” on percent_NA to see which rows have more then 50% NAs. We then remove all rows containing more then 50% using negative indexing.
percent_NA <- N_NA/N_SNPs*100
# Call which() on percent_NA
i_NA_50percent <- which(percent_NA > 50)
snps_num_t02 <- snps_num_t[-i_NA_50percent, ]Renaming the rows
Using “gsub()” we can shorten the names of the row names to make them better to read in analysis. This is done by getting rid of the first two elements of the three element name. For example, we would get rid of the “sample_TTAGGC” in “sample_TTAGGC_Div4” just to get “Div4”. This process also makes it easier to sort the different samples.
row_names <- row.names(snps_num_t02) # Key
row_names02 <- gsub("sample_","",row_names)
sample_id <- gsub("^([ATCG]*)(_)(.*)",
"\\3",
row_names02)
pop_id <- gsub("[01-9]*",
"",
sample_id)
table(pop_id) ## pop_id
## Alt Cau Div Nel Sub
## 15 12 15 15 11Removing invarient columns
The function “invar_omit” removes all columns in the data that are “fixed” or unchanged.
invar_omit <- function(x){
cat("Dataframe of dim",dim(x), "processed...\n")
sds <- apply(x, 2, sd, na.rm = TRUE)
i_var0 <- which(sds == 0)
cat(length(i_var0),"columns removed\n")
if(length(i_var0) > 0){
x <- x[, -i_var0]
}
## add return() with x in it
return(x)
}
snps_no_invar <- invar_omit(snps_num_t02) ## Dataframe of dim 68 1929 processed...
## 591 columns removedsnps_no_invar## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
## sample_ACAAA_Nel3 1 0 0 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 1 0 0 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 1 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0 0 1 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 1 0 0 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 1 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 1 0 0 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 1 0 0 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 1 0 0 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 1 0 0 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 1 0 0 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Sub15 NA 0 0 0 NA 0 NA 0 0 0 NA
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 0 0 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 NA NA 0 0 0 0 0 0 0 NA
## sample_CGATGT_Sub6 NA 0 0 0 0 0 0 NA 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 NA 0 0 NA 0 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 0 0 0 0 NA NA 0 NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 1 0 0 0
## sample_ACAGTG_Cau2 NA 0 1 0 0 0 0 0 1 NA 1
## sample_ACAGTG_Cau3 0 0 1 0 0 0 0 0 1 0 1
## sample_ACTAT_Cau11 0 0 1 0 0 1 0 0 1 0 1
## sample_ACTAT_Cau9 0 0 1 0 0 0 0 0 1 0 1
## sample_AGCCC_Cau7 0 0 1 0 0 0 0 0 1 0 1
## sample_ATGAAAC_Cau12 NA 0 1 0 0 0 0 0 1 0 NA
## sample_CTAGC_Cau5 0 0 1 0 0 NA 0 0 1 0 1
## sample_CTGTA_Cau8 NA 0 1 0 0 0 NA 0 NA 0 NA
## sample_GGACCTA_Cau13 0 0 1 0 0 0 0 0 1 0 1
## sample_TCACC_Cau1 0 1 1 0 0 0 0 0 1 0 1
## sample_TCACC_Cau4 0 0 1 0 0 0 0 0 1 0 1
## sample_TGACCA_Cau6 0 0 1 0 0 0 0 0 1 0 1
## sample_AAAAGTT_Div12 0 0 1 0 0 0 0 0 1 0 1
## sample_AAAAGTT_Div13 0 0 1 0 0 0 0 0 1 0 1
## sample_ACTAT_Div14 0 0 1 0 0 0 0 0 1 0 1
## sample_AGCAT_Div11 0 0 1 1 0 0 0 0 1 0 1
## sample_AGCCC_Div9 0 0 1 0 0 0 0 0 1 0 1
## sample_ATCACG_Div1 0 0 1 0 0 0 NA 0 1 0 1
## sample_ATGAAAC_Div8 0 0 1 0 0 0 0 0 1 0 NA
## sample_CGATGT_Div3 0 0 1 1 0 0 0 0 1 0 1
## sample_CTAGC_Div2 0 0 1 0 0 0 0 0 1 0 1
## sample_CTTGA_Div6 0 0 1 0 0 0 0 0 1 0 1
## sample_CTTGCTT_Div15 0 0 1 0 0 0 0 0 1 0 1
## sample_GTATT_Div10 0 0 1 0 0 0 0 0 1 0 1
## sample_GTATT_Div7 0 0 1 0 0 0 0 0 1 0 NA
## sample_TGACCA_Div5 0 0 1 0 0 0 0 0 1 0 1
## sample_TTAGGC_Div4 0 0 1 0 0 0 0 0 1 0 1
## [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20]
## sample_ACAAA_Nel3 0 0 0 1 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 1 1 0 0 0
## sample_AGCAT_Nel8 0 0 0 1 0 1 0 1 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 1 1 1 0
## sample_ATGAAAC_Nel15 0 0 0 1 0 1 0 1 0
## sample_CGATGT_Nel4 0 0 0 0 1 1 0 0 0
## sample_CTAGC_Nel7 0 0 0 1 0 1 0 0 0
## sample_CTGTA_Nel12 0 0 0 1 0 1 0 1 0
## sample_CTGTA_Nel9 0 0 0 0 0 1 0 0 0
## sample_CTTGA_Nel2 0 0 NA 1 0 1 0 1 0
## sample_GGACCTA_Nel11 0 0 1 1 0 1 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 1 0 1 0
## sample_GTATT_Nel14 0 0 0 1 0 1 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 1 1 1 0
## sample_TGACCA_Nel1 0 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 1 0 1 0 1 0
## sample_ACAGTG_Alt3 0 0 0 0 0 1 0 0 0
## sample_AGCCC_Alt13 0 0 0 1 0 1 0 0 0
## sample_ATCACG_Alt5 0 0 0 1 0 1 0 0 0
## sample_ATCACG_Alt7 0 0 0 1 0 1 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 1 0 1 0
## sample_CTGTA_Alt14 0 0 0 1 0 1 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 1 0 1 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0 1
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 NA NA 0 NA NA NA NA NA
## sample_ACAAA_Sub1 1 0 NA 0 0 NA NA NA NA
## sample_ACTAT_Sub7 0 0 0 0 0 1 1 1 0
## sample_AGCAT_Sub13 0 0 0 0 0 1 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 NA 0 0 NA NA NA NA 0
## sample_CTTGCTT_Sub14 1 0 0 0 NA 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 1 0 1 0 0 0
## sample_GTATT_Sub12 0 NA 0 0 NA 1 0 0 NA
## sample_TGACCA_Sub2 1 0 0 0 0 1 0 0 0
## sample_ACAGTG_Cau2 1 1 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 1 NA 0 0 0 0 1 0 0
## sample_ACTAT_Cau11 1 1 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 1 1 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 1 NA 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 NA NA NA 0 0 0 0 0 NA
## sample_CTAGC_Cau5 1 1 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 1 NA NA 0 NA NA NA NA NA
## sample_GGACCTA_Cau13 1 NA 0 0 0 0 0 0 0
## sample_TCACC_Cau1 1 1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 1 1 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 1 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 1 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 1 1 0 0 0 0 0 0 0
## sample_ACTAT_Div14 1 1 0 0 0 0 0 0 0
## sample_AGCAT_Div11 1 1 0 0 0 0 0 0 0
## sample_AGCCC_Div9 1 1 0 0 0 0 0 0 0
## sample_ATCACG_Div1 1 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 1 1 0 0 0 0 0 0 0
## sample_CGATGT_Div3 1 1 0 0 0 0 0 0 0
## sample_CTAGC_Div2 1 1 0 0 0 0 0 0 0
## sample_CTTGA_Div6 1 1 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 1 0 NA 0 0 0 0 0 0
## sample_GTATT_Div10 1 1 NA 0 0 0 0 0 0
## sample_GTATT_Div7 1 1 0 0 0 0 0 0 0
## sample_TGACCA_Div5 1 1 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 1 1 0 0 0 0 0 0 0
## [,21] [,22] [,23] [,24] [,25] [,26] [,27] [,28] [,29]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 1 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 NA NA 0 NA 0 0 NA
## sample_ACAAA_Sub1 1 0 0 0 0 0 0 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0 1
## sample_AGCCC_Sub11 0 0 NA 0 0 0 NA NA 0
## sample_CGATGT_Sub6 0 0 0 0 0 NA 0 0 0
## sample_CTTGCTT_Sub14 0 0 NA 0 0 0 NA NA 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 NA 0 NA NA 0 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 1 0 0
## sample_ACAGTG_Cau2 0 NA 0 0 0 0 1 0 0
## sample_ACAGTG_Cau3 0 1 0 0 0 0 1 0 0
## sample_ACTAT_Cau11 0 1 1 0 0 0 1 0 0
## sample_ACTAT_Cau9 0 1 0 0 0 0 1 0 0
## sample_AGCCC_Cau7 0 NA 0 0 0 0 NA NA 0
## sample_ATGAAAC_Cau12 0 NA NA 0 0 0 1 0 0
## sample_CTAGC_Cau5 0 1 0 0 0 0 1 0 0
## sample_CTGTA_Cau8 0 NA 1 0 0 0 1 0 0
## sample_GGACCTA_Cau13 0 NA 0 0 0 0 1 0 0
## sample_TCACC_Cau1 0 1 0 0 0 0 1 1 0
## sample_TCACC_Cau4 0 1 NA 0 0 0 1 1 0
## sample_TGACCA_Cau6 0 1 0 0 0 0 1 0 0
## sample_AAAAGTT_Div12 0 1 0 0 0 0 1 1 0
## sample_AAAAGTT_Div13 0 1 1 0 0 0 1 1 0
## sample_ACTAT_Div14 0 1 0 0 0 0 1 0 0
## sample_AGCAT_Div11 0 NA 0 0 0 0 1 1 0
## sample_AGCCC_Div9 0 1 0 0 0 0 1 1 0
## sample_ATCACG_Div1 0 NA 0 0 0 0 1 0 0
## sample_ATGAAAC_Div8 0 NA 0 0 0 0 1 0 0
## sample_CGATGT_Div3 0 1 0 0 0 0 1 1 0
## sample_CTAGC_Div2 0 1 0 0 0 0 1 0 0
## sample_CTTGA_Div6 0 1 1 0 0 0 1 0 0
## sample_CTTGCTT_Div15 0 NA 0 0 0 0 1 0 0
## sample_GTATT_Div10 0 1 0 0 0 0 1 0 0
## sample_GTATT_Div7 0 NA 0 0 0 0 1 1 0
## sample_TGACCA_Div5 0 1 0 0 0 0 1 1 0
## sample_TTAGGC_Div4 0 1 0 0 0 0 1 0 0
## [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 NA 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 NA 0 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 1 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 1 0 0 0 0 0 1 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 1 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 1 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 NA 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 1 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 NA 0 0 NA 0 NA 0
## sample_ACAAA_Sub1 0 0 NA 0 0 0 0 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 NA 0 NA 0 0 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 NA 0 0 NA NA
## sample_TGACCA_Sub2 0 0 NA 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA NA 0 1 NA 0 NA 0 NA
## sample_ACAGTG_Cau3 0 1 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 1 0 1 0 0 0 0 0
## sample_ACTAT_Cau9 0 1 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 NA NA NA 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 1 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 NA NA NA 1 NA 0 0 0 0
## sample_GGACCTA_Cau13 0 1 1 1 0 0 1 0 0
## sample_TCACC_Cau1 0 1 0 1 0 0 0 0 0
## sample_TCACC_Cau4 1 1 NA 0 0 1 0 0 0
## sample_TGACCA_Cau6 0 1 1 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 1 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 1 1 0 0 0 0 0 0
## sample_AGCAT_Div11 0 1 NA 0 NA 0 0 0 NA
## sample_AGCCC_Div9 0 1 0 1 0 0 0 0 0
## sample_ATCACG_Div1 0 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 1 0 0 0 0 1 0 0
## sample_CGATGT_Div3 0 1 1 1 0 0 0 0 0
## sample_CTAGC_Div2 1 1 0 0 NA 0 1 0 0
## sample_CTTGA_Div6 0 1 0 0 1 0 0 0 0
## sample_CTTGCTT_Div15 0 1 0 0 0 0 0 0 NA
## sample_GTATT_Div10 0 1 NA 1 0 0 0 0 0
## sample_GTATT_Div7 0 1 0 0 0 0 1 0 0
## sample_TGACCA_Div5 0 1 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 1 1 0 0 1 0 0 0 0
## [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47]
## sample_ACAAA_Nel3 0 0 1 0 0 0 1 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 1 1 0 0
## sample_AGCAT_Nel8 0 0 1 0 0 0 0 1 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 1 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 NA 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 1 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 1 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 1 0 0
## sample_GGACCTA_Nel13 0 0 1 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 1 0 0
## sample_ACAGTG_Alt3 0 0 1 0 0 0 1 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 1 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 1 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 1 1 0 0
## sample_AAAAGTT_Sub15 NA 0 NA NA NA NA NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 NA NA NA 0
## sample_ACTAT_Sub7 0 0 1 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0 NA
## sample_CGATGT_Sub6 NA 0 NA 0 NA NA NA 0 0
## sample_CTTGCTT_Sub14 0 0 NA 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 1 0 NA 1 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA NA NA NA 1 0 0 0
## sample_TGACCA_Sub2 NA 0 0 0 0 0 1 0 0
## sample_ACAGTG_Cau2 1 NA NA 0 1 0 0 0 0
## sample_ACAGTG_Cau3 1 NA 0 1 0 0 0 0 1
## sample_ACTAT_Cau11 1 1 0 0 0 0 0 0 NA
## sample_ACTAT_Cau9 1 0 0 0 1 0 0 0 0
## sample_AGCCC_Cau7 1 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Cau12 1 1 0 0 1 0 0 0 NA
## sample_CTAGC_Cau5 1 1 0 0 1 0 0 0 0
## sample_CTGTA_Cau8 NA NA 0 0 NA 0 0 NA NA
## sample_GGACCTA_Cau13 1 NA 0 0 1 0 0 0 NA
## sample_TCACC_Cau1 0 0 0 0 1 0 0 0 1
## sample_TCACC_Cau4 1 NA 0 0 0 0 0 0 1
## sample_TGACCA_Cau6 1 0 0 0 0 0 0 0 1
## sample_AAAAGTT_Div12 1 NA 0 0 1 0 0 0 1
## sample_AAAAGTT_Div13 1 1 0 0 0 0 0 0 1
## sample_ACTAT_Div14 1 0 0 0 0 0 0 0 1
## sample_AGCAT_Div11 1 NA NA 0 0 0 0 0 1
## sample_AGCCC_Div9 1 0 0 0 1 0 0 0 1
## sample_ATCACG_Div1 1 1 0 0 1 0 0 0 1
## sample_ATGAAAC_Div8 1 NA 0 0 1 0 0 0 1
## sample_CGATGT_Div3 1 1 0 0 0 0 0 0 1
## sample_CTAGC_Div2 1 0 0 0 1 0 0 0 0
## sample_CTTGA_Div6 1 1 0 0 1 0 0 0 1
## sample_CTTGCTT_Div15 1 1 0 0 1 0 0 0 NA
## sample_GTATT_Div10 1 NA NA 0 1 0 0 0 NA
## sample_GTATT_Div7 1 1 NA 0 1 0 0 0 0
## sample_TGACCA_Div5 1 0 0 0 1 0 0 0 0
## sample_TTAGGC_Div4 1 0 0 0 1 0 0 0 1
## [,48] [,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 1 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 1 0 1 0
## sample_ATGAAAC_Nel10 0 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 1 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 1 0
## sample_CTGTA_Nel12 0 0 0 0 0 1 0 1 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 1 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel13 0 0 0 0 0 1 0 0 0
## sample_GTATT_Nel14 0 0 0 0 1 0 0 1 0
## sample_TCACC_Nel6 0 1 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 1 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0 1
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 1 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 1 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 0 0 0 NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 1 NA 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 1 0
## sample_AGCAT_Sub13 0 0 0 0 0 1 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 NA 0 0 NA 0 0 0 1 NA
## sample_CTTGCTT_Sub14 0 0 0 NA NA NA NA 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 1 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 1 NA 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 1 0 0 0
## sample_ACAGTG_Cau2 1 0 0 0 0 1 NA 0 0
## sample_ACAGTG_Cau3 1 0 0 0 0 1 1 NA 0
## sample_ACTAT_Cau11 1 0 0 1 0 1 1 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 1 1 1 0
## sample_AGCCC_Cau7 1 0 0 0 0 1 1 0 0
## sample_ATGAAAC_Cau12 1 0 0 NA 0 1 NA NA 0
## sample_CTAGC_Cau5 1 0 0 0 0 1 1 0 0
## sample_CTGTA_Cau8 1 0 0 0 0 1 1 0 0
## sample_GGACCTA_Cau13 1 0 0 0 0 1 1 0 0
## sample_TCACC_Cau1 1 0 1 1 0 1 1 0 0
## sample_TCACC_Cau4 1 0 0 0 0 1 1 0 0
## sample_TGACCA_Cau6 1 0 0 0 0 1 1 0 0
## sample_AAAAGTT_Div12 1 0 0 1 0 1 1 0 0
## sample_AAAAGTT_Div13 1 0 0 1 0 1 NA 1 0
## sample_ACTAT_Div14 1 0 0 0 0 1 1 0 0
## sample_AGCAT_Div11 1 0 0 0 0 1 NA 0 0
## sample_AGCCC_Div9 1 0 0 0 0 1 NA 0 0
## sample_ATCACG_Div1 1 0 0 1 0 1 1 0 0
## sample_ATGAAAC_Div8 1 0 1 0 0 1 1 0 0
## sample_CGATGT_Div3 0 0 0 0 0 1 1 0 0
## sample_CTAGC_Div2 1 0 0 1 0 1 1 0 0
## sample_CTTGA_Div6 1 0 0 0 0 1 1 0 0
## sample_CTTGCTT_Div15 1 0 0 0 0 1 1 NA 0
## sample_GTATT_Div10 1 0 0 0 0 1 NA 0 0
## sample_GTATT_Div7 1 0 0 0 0 1 1 0 0
## sample_TGACCA_Div5 1 0 0 0 0 1 1 0 0
## sample_TTAGGC_Div4 1 0 0 1 0 1 1 0 0
## [,57] [,58] [,59] [,60] [,61] [,62] [,63] [,64] [,65]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0 1
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0 1
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 1 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 1 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 1 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 1 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 1 0 0 0 0 0 0 0 1
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 1 0 1 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 1 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 0 0 0 NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 NA NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 1 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 1 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 0 NA NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 NA 0 0
## sample_ACAGTG_Cau2 0 0 1 0 1 0 0 0 0
## sample_ACAGTG_Cau3 0 0 1 0 1 0 0 0 0
## sample_ACTAT_Cau11 0 0 1 0 1 0 0 0 0
## sample_ACTAT_Cau9 0 0 1 0 1 0 0 0 0
## sample_AGCCC_Cau7 0 0 1 0 1 0 0 NA 0
## sample_ATGAAAC_Cau12 0 0 1 0 1 0 0 0 0
## sample_CTAGC_Cau5 0 0 1 0 1 0 0 1 0
## sample_CTGTA_Cau8 0 0 1 0 1 0 NA 0 NA
## sample_GGACCTA_Cau13 0 0 1 0 1 0 0 0 0
## sample_TCACC_Cau1 0 0 1 0 1 0 0 0 0
## sample_TCACC_Cau4 0 0 1 0 1 0 0 NA 0
## sample_TGACCA_Cau6 0 0 1 0 1 0 0 0 0
## sample_AAAAGTT_Div12 0 0 1 0 1 0 0 0 0
## sample_AAAAGTT_Div13 0 0 1 0 1 0 0 0 0
## sample_ACTAT_Div14 0 0 1 0 1 0 0 0 0
## sample_AGCAT_Div11 0 0 1 0 1 0 0 0 0
## sample_AGCCC_Div9 0 0 1 0 1 0 0 0 0
## sample_ATCACG_Div1 0 0 1 0 1 0 0 0 0
## sample_ATGAAAC_Div8 0 0 1 0 1 0 0 0 0
## sample_CGATGT_Div3 0 0 1 0 1 0 0 0 0
## sample_CTAGC_Div2 0 0 1 0 1 0 0 0 0
## sample_CTTGA_Div6 0 0 1 0 1 0 0 0 0
## sample_CTTGCTT_Div15 0 0 1 0 1 0 0 0 NA
## sample_GTATT_Div10 0 0 1 0 1 0 0 0 0
## sample_GTATT_Div7 0 0 1 0 1 0 NA 0 0
## sample_TGACCA_Div5 0 NA 1 0 1 0 0 0 0
## sample_TTAGGC_Div4 0 0 1 0 1 0 0 0 0
## [,66] [,67] [,68] [,69] [,70] [,71] [,72] [,73] [,74]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 NA NA 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 1 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 1 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 1 0 0
## sample_GGACCTA_Nel11 0 0 1 0 1 0 0 1 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 1 0 0
## sample_TCACC_Nel6 0 NA NA NA NA NA 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 NA NA 1
## sample_ACAGTG_Alt3 0 0 0 1 0 0 0 0 0
## sample_AGCCC_Alt13 0 NA NA NA NA NA 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 1 0 0 0 NA NA 0
## sample_CTTGA_Alt10 0 0 0 0 0 1 0 1 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 1 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 1 0 1 0
## sample_AAAAGTT_Sub15 NA 1 0 0 0 0 0 0 NA
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 NA NA NA NA NA 0 0 0
## sample_AGCCC_Sub11 NA NA NA NA NA NA 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0 NA
## sample_CTTGCTT_Sub14 NA 0 0 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 1 0 1 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 0 0 0 NA
## sample_TGACCA_Sub2 0 1 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA 0 0 0 0 0 0 0 NA
## sample_ACAGTG_Cau3 0 NA NA NA NA NA 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 NA NA NA NA NA 0 0 0
## sample_ATGAAAC_Cau12 NA 0 0 0 0 0 0 0 NA
## sample_CTAGC_Cau5 0 NA NA NA NA NA 0 0 0
## sample_CTGTA_Cau8 NA 0 0 1 0 0 0 0 NA
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 NA NA NA NA NA 0 0 0
## sample_TCACC_Cau4 NA 0 0 0 0 0 0 0 NA
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0 NA
## sample_AAAAGTT_Div13 1 0 0 0 0 0 0 0 NA
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 NA 0 0 0 0 0 0 0 NA
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 NA 1 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0 NA
## sample_CTAGC_Div2 0 NA 0 1 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 0 0 NA
## sample_GTATT_Div10 0 0 0 0 0 0 0 0 NA
## sample_GTATT_Div7 0 0 0 1 0 0 0 0 NA
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0 0
## [,75] [,76] [,77] [,78] [,79] [,80] [,81] [,82] [,83]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 NA 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 NA 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 NA 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 1 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 NA 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 NA 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 NA 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 NA 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 0 NA 0 NA 0 0
## sample_ACAAA_Sub1 NA 0 0 0 0 NA 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0 1
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 1 0 0 0 0 0 0 1
## sample_CGATGT_Sub6 NA 0 0 0 0 0 NA 0 0
## sample_CTTGCTT_Sub14 0 NA 0 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA 0 0 0 0 NA 0 0
## sample_TGACCA_Sub2 0 NA 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA NA 0 0 0 0 0 0 1
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0 1
## sample_ACTAT_Cau11 1 0 1 0 0 0 0 0 1
## sample_ACTAT_Cau9 0 0 0 0 0 0 1 0 1
## sample_AGCCC_Cau7 0 0 NA NA 0 0 0 0 1
## sample_ATGAAAC_Cau12 NA NA 0 0 0 0 0 0 1
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0 1
## sample_CTGTA_Cau8 NA NA 0 0 NA 0 NA 0 1
## sample_GGACCTA_Cau13 0 0 NA NA 0 0 0 0 1
## sample_TCACC_Cau1 1 0 0 0 0 0 0 0 1
## sample_TCACC_Cau4 NA 0 0 0 0 0 0 0 1
## sample_TGACCA_Cau6 1 0 0 0 0 0 0 0 1
## sample_AAAAGTT_Div12 NA 0 0 0 0 0 0 0 1
## sample_AAAAGTT_Div13 NA 0 1 0 0 0 1 0 1
## sample_ACTAT_Div14 0 0 0 0 0 1 0 0 1
## sample_AGCAT_Div11 NA NA 0 0 1 NA 0 0 1
## sample_AGCCC_Div9 0 0 1 0 0 0 0 0 1
## sample_ATCACG_Div1 0 0 0 0 0 0 1 0 1
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0 1
## sample_CGATGT_Div3 NA 0 0 0 0 0 0 0 1
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0 1
## sample_CTTGA_Div6 0 0 0 0 0 0 1 0 1
## sample_CTTGCTT_Div15 NA 0 0 0 0 0 1 0 1
## sample_GTATT_Div10 NA 0 0 0 0 0 0 0 1
## sample_GTATT_Div7 NA NA 0 0 0 NA 0 0 1
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0 1
## sample_TTAGGC_Div4 1 0 0 0 0 0 0 0 1
## [,84] [,85] [,86] [,87] [,88] [,89] [,90] [,91] [,92]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 1 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0 1
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 1 0 0 0 0
## sample_CTGTA_Nel12 1 0 0 0 1 0 0 1 0
## sample_CTGTA_Nel9 1 0 0 0 1 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 1 0 1 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 1 0 0 1 1
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 1 0
## sample_ACAAA_Alt11 1 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 1 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 1 0 0 0 1 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 0 0
## sample_GCCAAT_Alt9 1 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt2 1 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 1 0 0 0 0 0 0 1 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 0 0 0 NA 0 0
## sample_ACAAA_Sub1 0 0 0 0 0 0 NA 0 0
## sample_ACTAT_Sub7 1 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 1 0 0 0 0 0 1 0 0
## sample_AGCCC_Sub11 NA 0 NA 0 0 0 NA 0 0
## sample_CGATGT_Sub6 0 NA 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA 0 NA 0 0 NA 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 NA 0 0
## sample_GTATT_Sub12 NA NA NA 0 0 NA 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 NA NA 0 0 NA 0 NA 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 1 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 1 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 1 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 NA 1 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 NA 0 1 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 1 0
## sample_CTGTA_Cau8 0 0 0 0 0 0 NA 1 0
## sample_GGACCTA_Cau13 0 NA 0 0 0 0 NA 1 0
## sample_TCACC_Cau1 0 1 0 0 0 0 0 1 0
## sample_TCACC_Cau4 0 0 NA 0 0 0 NA 1 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Div13 0 0 0 0 0 NA 0 1 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 1 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0 1 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 1 0
## sample_ATCACG_Div1 0 0 0 0 0 0 NA 1 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 NA 1 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 1 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 1 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 1 0
## sample_CTTGCTT_Div15 0 NA 0 0 0 0 0 1 0
## sample_GTATT_Div10 0 0 0 0 0 0 0 1 0
## sample_GTATT_Div7 0 0 0 0 0 0 0 1 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 1 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 1 0
## [,93] [,94] [,95] [,96] [,97] [,98] [,99] [,100] [,101]
## sample_ACAAA_Nel3 0 0 0 1 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 1 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 1 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 1 0 0
## sample_CTTGA_Nel2 0 0 1 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0 1
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 1 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0 1
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 1 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 1 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 NA NA 0 NA NA 0 NA NA
## sample_ACAAA_Sub1 0 0 0 0 NA NA 0 NA 0
## sample_ACTAT_Sub7 0 0 0 0 1 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 NA NA 0 0 NA
## sample_CGATGT_Sub6 0 NA NA 0 0 0 0 NA 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 0 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 1 0 0 0 0
## sample_GTATT_Sub12 0 NA NA 0 NA NA NA NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0 NA
## sample_ACAGTG_Cau2 0 0 1 0 NA NA 0 1 NA
## sample_ACAGTG_Cau3 0 NA NA 0 0 1 0 NA 0
## sample_ACTAT_Cau11 0 1 1 0 1 0 0 1 0
## sample_ACTAT_Cau9 0 0 1 0 1 0 0 1 NA
## sample_AGCCC_Cau7 0 0 1 0 1 0 0 1 NA
## sample_ATGAAAC_Cau12 1 0 1 0 NA NA 0 NA 0
## sample_CTAGC_Cau5 0 1 1 0 1 0 0 0 0
## sample_CTGTA_Cau8 1 NA NA 0 NA NA 0 NA NA
## sample_GGACCTA_Cau13 0 0 1 0 NA NA 0 1 0
## sample_TCACC_Cau1 0 0 1 0 1 0 0 0 NA
## sample_TCACC_Cau4 NA 0 1 0 NA NA 0 1 0
## sample_TGACCA_Cau6 0 0 1 0 1 0 0 0 0
## sample_AAAAGTT_Div12 0 0 1 0 0 1 0 1 0
## sample_AAAAGTT_Div13 0 0 1 0 1 0 0 0 NA
## sample_ACTAT_Div14 0 NA NA 0 1 0 0 0 0
## sample_AGCAT_Div11 0 0 1 0 NA NA 0 NA 0
## sample_AGCCC_Div9 0 0 1 0 1 0 0 1 NA
## sample_ATCACG_Div1 0 0 1 0 NA NA 0 NA NA
## sample_ATGAAAC_Div8 0 0 1 0 NA NA 0 1 NA
## sample_CGATGT_Div3 1 0 1 0 0 0 0 1 0
## sample_CTAGC_Div2 0 NA NA 0 1 0 0 0 NA
## sample_CTTGA_Div6 1 0 1 0 1 0 0 0 0
## sample_CTTGCTT_Div15 0 0 1 0 NA NA 0 NA NA
## sample_GTATT_Div10 0 0 1 0 1 0 0 1 0
## sample_GTATT_Div7 1 NA NA 0 1 0 0 NA NA
## sample_TGACCA_Div5 1 0 1 0 1 0 0 0 0
## sample_TTAGGC_Div4 0 0 1 0 1 0 0 1 0
## [,102] [,103] [,104] [,105] [,106] [,107] [,108] [,109]
## sample_ACAAA_Nel3 0 0 0 1 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 1 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 1 0 NA NA 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 1 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 NA NA 0
## sample_CTGTA_Nel9 0 0 1 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 1 0 1 0 0 0
## sample_GGACCTA_Nel11 0 0 1 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 1 0 0 NA NA 0
## sample_GTATT_Nel14 0 0 0 0 1 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 0 1 1 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 1 0 0 0
## sample_CTGTA_Alt14 0 0 1 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 1 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 1 0 0 0 0 0
## sample_GCCAAT_Alt9 0 NA 0 0 1 0 0 0
## sample_TTAGGC_Alt2 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA 0 NA NA 0 NA NA 0
## sample_ACAAA_Sub1 0 0 0 0 0 NA NA 0
## sample_ACTAT_Sub7 1 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 1 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 NA 0 NA NA 0 NA NA 0
## sample_CGATGT_Sub6 0 NA NA NA 0 0 0 0
## sample_CTTGCTT_Sub14 NA 0 0 0 NA 0 0 0
## sample_GAATTCA_Sub9 0 0 0 1 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 NA 0 0 0
## sample_TGACCA_Sub2 NA 0 0 0 NA 0 0 0
## sample_ACAGTG_Cau2 NA 0 0 0 0 1 0 NA
## sample_ACAGTG_Cau3 1 0 1 0 0 0 0 1
## sample_ACTAT_Cau11 1 0 1 0 0 0 0 1
## sample_ACTAT_Cau9 NA 0 0 0 0 0 0 1
## sample_AGCCC_Cau7 NA NA NA NA 0 NA NA 1
## sample_ATGAAAC_Cau12 1 0 0 0 0 NA NA 1
## sample_CTAGC_Cau5 1 0 1 0 0 0 0 1
## sample_CTGTA_Cau8 NA NA 0 0 0 0 0 1
## sample_GGACCTA_Cau13 1 0 0 0 0 0 0 1
## sample_TCACC_Cau1 NA NA 1 0 0 1 0 1
## sample_TCACC_Cau4 1 1 0 0 NA NA NA 1
## sample_TGACCA_Cau6 1 0 1 0 0 0 0 1
## sample_AAAAGTT_Div12 1 0 0 0 0 1 0 1
## sample_AAAAGTT_Div13 NA 0 1 0 0 1 0 1
## sample_ACTAT_Div14 1 0 1 0 0 0 0 1
## sample_AGCAT_Div11 1 0 0 0 0 1 1 1
## sample_AGCCC_Div9 NA 0 0 0 0 0 0 1
## sample_ATCACG_Div1 NA 0 0 0 0 0 1 1
## sample_ATGAAAC_Div8 NA 0 0 0 0 1 0 1
## sample_CGATGT_Div3 1 0 0 0 0 1 0 1
## sample_CTAGC_Div2 NA 0 0 0 0 1 0 1
## sample_CTTGA_Div6 1 0 1 0 0 1 0 1
## sample_CTTGCTT_Div15 NA NA 1 0 0 NA NA 1
## sample_GTATT_Div10 1 0 0 0 0 1 0 1
## sample_GTATT_Div7 NA NA 0 0 0 1 0 1
## sample_TGACCA_Div5 1 0 0 0 0 1 1 1
## sample_TTAGGC_Div4 1 0 0 0 0 1 0 1
## [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117]
## sample_ACAAA_Nel3 0 0 0 0 0 0 1 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 1 0
## sample_AGCAT_Nel8 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 1 0
## sample_CTAGC_Nel7 0 0 1 0 1 0 1 1
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 1 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 1 0
## sample_TCACC_Nel6 0 0 0 0 0 0 1 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 1 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 1 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 1 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Sub15 0 NA NA NA NA NA NA 0
## sample_ACAAA_Sub1 0 NA NA NA NA NA 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 NA NA NA NA NA 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 1 0 0
## sample_GGACCTA_Sub10 1 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA NA NA NA NA 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 1 NA NA NA NA NA 0 NA
## sample_ACAGTG_Cau3 1 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 1 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 NA NA NA NA NA NA 0 NA
## sample_CTAGC_Cau5 1 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 NA NA NA NA NA NA 0 0
## sample_GGACCTA_Cau13 1 NA NA NA NA NA 0 0
## sample_TCACC_Cau1 1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 1 0 0 0 0 0 0 NA
## sample_TGACCA_Cau6 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 1 1 0 0 0 0 0 0
## sample_ACTAT_Div14 1 0 0 0 0 0 0 0
## sample_AGCAT_Div11 1 NA NA NA NA NA 0 NA
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 1 NA NA NA NA NA 0 0
## sample_ATGAAAC_Div8 1 NA NA NA NA NA 0 0
## sample_CGATGT_Div3 1 0 0 0 0 0 0 0
## sample_CTAGC_Div2 1 0 0 0 0 0 0 0
## sample_CTTGA_Div6 1 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 NA NA NA NA NA NA 0 0
## sample_GTATT_Div10 1 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 NA NA NA NA NA 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 1 0 0 0 0 0 0 0
## [,118] [,119] [,120] [,121] [,122] [,123] [,124] [,125]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 1 0 0 0 0 0
## sample_AGCAT_Nel8 0 1 1 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 1 0 0 0 0 0
## sample_CTAGC_Nel7 0 1 1 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 1 0 0 0 0 0
## sample_CTGTA_Nel9 0 1 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 1 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 1 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 1 1 0 0 0 0 0
## sample_GTATT_Nel14 0 1 1 0 0 0 0 0
## sample_TCACC_Nel6 0 1 1 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 1 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 1 0 0 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 1 1 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 1 1 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 1 1 0 0 0 0 0
## sample_GCCAAT_Alt9 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 1 0 0 1 0 0
## sample_TTAGGC_Alt6 0 1 1 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 NA NA NA NA 0 NA 0
## sample_ACAAA_Sub1 0 NA NA NA 0 0 NA 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 1 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 NA NA NA 0 0 0
## sample_CTTGCTT_Sub14 0 NA 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 1 0 0 0 0 0
## sample_GGACCTA_Sub10 0 1 1 0 0 0 0 1
## sample_GTATT_Sub12 NA NA 1 0 NA 0 0 0
## sample_TGACCA_Sub2 0 1 1 0 0 0 0 0
## sample_ACAGTG_Cau2 NA 0 NA NA NA 0 0 1
## sample_ACAGTG_Cau3 1 0 0 0 1 0 0 1
## sample_ACTAT_Cau11 1 0 0 0 1 0 0 1
## sample_ACTAT_Cau9 1 0 0 0 0 0 0 1
## sample_AGCCC_Cau7 1 0 0 0 NA 0 0 1
## sample_ATGAAAC_Cau12 NA 0 0 0 NA 0 0 1
## sample_CTAGC_Cau5 1 0 0 0 1 0 0 1
## sample_CTGTA_Cau8 1 NA 0 0 NA 0 0 1
## sample_GGACCTA_Cau13 1 0 NA NA 1 0 0 1
## sample_TCACC_Cau1 1 0 0 0 0 0 0 1
## sample_TCACC_Cau4 NA NA 0 0 0 0 0 1
## sample_TGACCA_Cau6 1 0 0 0 0 0 0 1
## sample_AAAAGTT_Div12 1 0 0 0 1 0 1 1
## sample_AAAAGTT_Div13 1 0 0 0 0 0 1 1
## sample_ACTAT_Div14 1 0 0 0 1 0 0 1
## sample_AGCAT_Div11 NA 0 0 0 0 0 1 1
## sample_AGCCC_Div9 1 0 0 0 0 0 1 1
## sample_ATCACG_Div1 1 0 0 0 1 0 NA 1
## sample_ATGAAAC_Div8 1 0 0 0 0 0 0 1
## sample_CGATGT_Div3 0 0 0 0 1 0 0 1
## sample_CTAGC_Div2 1 0 0 0 0 0 0 1
## sample_CTTGA_Div6 1 0 0 0 1 0 0 1
## sample_CTTGCTT_Div15 1 0 0 0 NA 0 0 1
## sample_GTATT_Div10 1 0 0 0 0 0 NA 1
## sample_GTATT_Div7 1 0 0 0 0 0 NA 1
## sample_TGACCA_Div5 1 0 0 0 1 0 1 1
## sample_TTAGGC_Div4 1 0 0 0 1 0 0 1
## [,126] [,127] [,128] [,129] [,130] [,131] [,132] [,133]
## sample_ACAAA_Nel3 0 0 0 1 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 1 0 NA 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 NA 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 1
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 1 0 1 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 1 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 1 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 NA 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 NA 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 NA 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 NA 0 0 NA 0 NA
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 NA 1
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 1
## sample_CTTGCTT_Sub14 0 0 0 0 0 NA 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 NA 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 NA 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 NA 0 1
## sample_ACAGTG_Cau2 0 0 0 0 0 0 1 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 1 0
## sample_ACTAT_Cau11 0 1 0 0 0 0 1 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 1 0
## sample_AGCCC_Cau7 0 0 0 0 1 0 1 0
## sample_ATGAAAC_Cau12 0 0 NA 0 0 NA 1 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 1 0
## sample_CTGTA_Cau8 0 NA 0 0 NA 0 1 0
## sample_GGACCTA_Cau13 0 0 0 0 0 NA 1 0
## sample_TCACC_Cau1 0 0 0 0 1 0 1 0
## sample_TCACC_Cau4 0 1 0 0 0 0 1 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Div13 0 1 0 0 0 0 1 0
## sample_ACTAT_Div14 0 0 0 0 0 0 1 0
## sample_AGCAT_Div11 0 0 0 0 0 0 1 0
## sample_AGCCC_Div9 0 0 0 0 0 0 1 0
## sample_ATCACG_Div1 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Div8 0 1 0 0 0 0 1 0
## sample_CGATGT_Div3 0 0 0 0 0 0 1 0
## sample_CTAGC_Div2 0 0 0 0 0 0 1 0
## sample_CTTGA_Div6 0 0 0 0 0 0 1 0
## sample_CTTGCTT_Div15 0 0 0 0 0 NA 1 0
## sample_GTATT_Div10 1 0 0 0 0 0 1 0
## sample_GTATT_Div7 0 0 0 0 0 0 1 0
## sample_TGACCA_Div5 0 0 0 0 0 0 1 0
## sample_TTAGGC_Div4 1 0 0 0 0 0 1 0
## [,134] [,135] [,136] [,137] [,138] [,139] [,140] [,141]
## sample_ACAAA_Nel3 0 0 1 0 0 0 0 1
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 1
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 1
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 1 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 1 0 0 0 0 1
## sample_GTATT_Nel14 1 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 1 0 0 0 0 1
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 1
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 1 0 0 0 0 1
## sample_AGCCC_Alt13 0 0 1 0 0 0 0 1
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 1
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 1
## sample_CGATGT_Alt1 1 0 0 0 0 0 0 1
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 1 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 1
## sample_GCCAAT_Alt9 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 1
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 1
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 1
## sample_AAAAGTT_Sub15 NA 0 0 0 0 NA NA 0
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 1
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 1
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 NA
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 1
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 1
## sample_GTATT_Sub12 0 0 0 0 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 1 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 1 0 0
## sample_ACTAT_Cau11 0 NA NA NA 0 1 0 0
## sample_ACTAT_Cau9 0 1 0 1 0 1 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 1 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 1 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 1 0 0
## sample_CTGTA_Cau8 NA 0 0 0 NA 1 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 1 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Div12 0 NA NA NA 0 1 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 1 0 0
## sample_ACTAT_Div14 0 1 1 1 0 1 0 0
## sample_AGCAT_Div11 0 0 0 0 0 1 0 0
## sample_AGCCC_Div9 0 1 0 1 0 1 0 0
## sample_ATCACG_Div1 0 1 0 1 0 0 0 0
## sample_ATGAAAC_Div8 0 NA NA NA 0 1 0 0
## sample_CGATGT_Div3 0 1 1 1 1 1 0 0
## sample_CTAGC_Div2 0 0 0 0 0 1 0 0
## sample_CTTGA_Div6 0 1 0 1 0 1 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 1 0 0
## sample_GTATT_Div10 0 1 1 1 0 1 0 0
## sample_GTATT_Div7 NA NA NA NA 0 1 0 0
## sample_TGACCA_Div5 0 1 0 1 1 1 0 0
## sample_TTAGGC_Div4 0 1 1 1 0 1 0 0
## [,142] [,143] [,144] [,145] [,146] [,147] [,148] [,149]
## sample_ACAAA_Nel3 0 0 0 0 0 0 1 0
## sample_ACAGTG_Nel5 0 0 0 0 1 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 1 0 0 1 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 1 0
## sample_CTGTA_Nel9 0 0 0 0 1 0 0 0
## sample_CTTGA_Nel2 0 0 0 1 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 1 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 1 0 1 0
## sample_GTATT_Nel14 0 0 0 0 1 0 1 0
## sample_TCACC_Nel6 0 0 0 0 1 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 1 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 1 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 1 0 0 0
## sample_ATCACG_Alt7 0 0 0 1 0 0 0 0
## sample_CGATGT_Alt1 0 0 1 1 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 1 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 1 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 NA 0 1 0 0 0 NA
## sample_ACAAA_Sub1 0 0 0 1 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 1 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 1
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 1
## sample_CGATGT_Sub6 0 0 0 0 1 0 0 NA
## sample_CTTGCTT_Sub14 0 NA 0 1 0 0 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 1 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 1 0 0 0
## sample_GTATT_Sub12 0 0 0 1 0 0 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 NA 0 0 0 0 0 NA
## sample_ACAGTG_Cau3 0 1 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 NA 0 0 0 NA NA 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 NA NA 0
## sample_CTAGC_Cau5 0 1 0 0 0 1 0 0
## sample_CTGTA_Cau8 0 0 0 0 0 NA NA NA
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 1 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 NA
## sample_AAAAGTT_Div13 1 1 0 0 0 0 0 0
## sample_ACTAT_Div14 0 1 0 0 0 1 0 0
## sample_AGCAT_Div11 0 1 0 0 0 0 0 NA
## sample_AGCCC_Div9 0 1 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 1 0 0 0 1 0 0
## sample_CGATGT_Div3 0 1 0 0 0 0 0 NA
## sample_CTAGC_Div2 0 1 0 0 0 0 0 0
## sample_CTTGA_Div6 0 1 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 0 0
## sample_GTATT_Div10 0 0 0 0 0 0 0 NA
## sample_GTATT_Div7 0 1 0 0 0 0 0 NA
## sample_TGACCA_Div5 0 1 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 NA 0 0 0 0 0 0
## [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 1
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0 1
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 1 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 1
## sample_ATCACG_Alt7 0 0 0 0 1 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 1 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 1
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 1
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 NA NA 0 0 0 0
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 NA NA NA 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA NA 0 0 NA 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA 0 0 NA NA 0 0
## sample_TGACCA_Sub2 NA NA 0 0 NA 0 0 0
## sample_ACAGTG_Cau2 1 0 0 1 NA NA 0 0
## sample_ACAGTG_Cau3 1 0 0 1 0 1 0 0
## sample_ACTAT_Cau11 1 0 0 1 0 1 0 0
## sample_ACTAT_Cau9 1 0 0 1 0 1 0 0
## sample_AGCCC_Cau7 1 0 0 1 0 NA NA 0
## sample_ATGAAAC_Cau12 1 0 0 1 NA 1 0 0
## sample_CTAGC_Cau5 1 0 0 1 0 1 0 0
## sample_CTGTA_Cau8 NA NA 0 1 0 1 NA 0
## sample_GGACCTA_Cau13 1 0 0 1 0 1 0 0
## sample_TCACC_Cau1 1 0 0 1 0 1 0 0
## sample_TCACC_Cau4 1 0 0 1 NA NA 0 0
## sample_TGACCA_Cau6 1 0 0 1 0 1 0 0
## sample_AAAAGTT_Div12 1 0 0 1 NA 1 0 0
## sample_AAAAGTT_Div13 1 0 0 1 0 1 0 0
## sample_ACTAT_Div14 1 0 1 1 0 1 0 0
## sample_AGCAT_Div11 1 0 0 1 NA 1 0 0
## sample_AGCCC_Div9 1 0 0 1 0 1 0 0
## sample_ATCACG_Div1 1 0 0 1 0 1 0 0
## sample_ATGAAAC_Div8 1 0 0 1 0 1 0 0
## sample_CGATGT_Div3 1 1 0 1 0 1 0 0
## sample_CTAGC_Div2 1 0 1 1 0 1 0 0
## sample_CTTGA_Div6 1 0 0 1 0 1 0 0
## sample_CTTGCTT_Div15 1 0 0 1 0 1 0 0
## sample_GTATT_Div10 1 0 0 1 NA 1 0 0
## sample_GTATT_Div7 1 0 0 1 0 1 NA 0
## sample_TGACCA_Div5 1 0 0 1 0 1 0 0
## sample_TTAGGC_Div4 1 0 0 1 0 1 0 0
## [,158] [,159] [,160] [,161] [,162] [,163] [,164] [,165]
## sample_ACAAA_Nel3 0 0 1 1 1 1 0 0
## sample_ACAGTG_Nel5 0 0 0 0 1 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 1 1 1 1 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 1 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 1 0 0 0
## sample_CTGTA_Alt14 0 0 1 1 1 1 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 1
## sample_TTAGGC_Alt2 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 NA NA NA NA NA 0 0
## sample_ACAAA_Sub1 0 NA NA NA NA NA 0 0
## sample_ACTAT_Sub7 0 1 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 1 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 NA NA NA NA NA 0 0
## sample_CGATGT_Sub6 NA NA NA NA NA NA 0 0
## sample_CTTGCTT_Sub14 NA 0 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 1 0 0 0 0 0 0
## sample_GGACCTA_Sub10 1 1 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 0 0 0
## sample_TGACCA_Sub2 NA 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 NA NA NA NA NA 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 0
## sample_ACTAT_Div14 NA 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 0 0
## sample_GTATT_Div10 0 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,166] [,167] [,168] [,169] [,170] [,171] [,172] [,173]
## sample_ACAAA_Nel3 1 1 0 0 0 0 0 1
## sample_ACAGTG_Nel5 0 1 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 1 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 1 1 0 0 0 0 0 1
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 1 0 0 0 0 1 0
## sample_CTAGC_Nel7 1 1 1 0 0 0 0 1
## sample_CTGTA_Nel12 1 0 0 0 1 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 1 0 0 0 0 0 1 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel13 1 1 0 0 0 0 0 1
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 1 0 0 0 1 0 0
## sample_TGACCA_Nel1 1 1 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 1 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 1 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 1 1 0 0 0 0 1 0
## sample_CTTGA_Alt10 1 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 1 0 0 0 1 0 1 1
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 1
## sample_AAAAGTT_Sub15 NA 0 0 NA NA NA NA NA
## sample_ACAAA_Sub1 0 1 0 NA NA 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 1 0 0 1 0 0 0
## sample_AGCCC_Sub11 0 1 0 0 0 0 0 0
## sample_CGATGT_Sub6 NA NA 0 0 0 NA 0 0
## sample_CTTGCTT_Sub14 0 1 0 NA NA NA 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 1 0 0 0 0 0 0 1
## sample_GTATT_Sub12 1 1 0 NA NA 0 0 0
## sample_TGACCA_Sub2 0 1 1 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 1 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 1 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 1 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 1 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 1 NA NA 0 0 0
## sample_ATGAAAC_Cau12 0 0 1 0 0 NA 0 0
## sample_CTAGC_Cau5 0 0 1 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 1 NA NA NA 0 0
## sample_GGACCTA_Cau13 0 0 1 0 0 0 0 0
## sample_TCACC_Cau1 0 0 1 NA NA 0 0 0
## sample_TCACC_Cau4 0 0 1 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 1 0 0 NA 0 0
## sample_AAAAGTT_Div13 0 0 1 0 0 0 0 0
## sample_ACTAT_Div14 0 0 1 0 0 0 0 0
## sample_AGCAT_Div11 0 0 1 0 0 0 0 0
## sample_AGCCC_Div9 0 0 1 0 0 0 0 0
## sample_ATCACG_Div1 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 1 0 0 0 0 0
## sample_CGATGT_Div3 0 0 1 0 0 0 0 0
## sample_CTAGC_Div2 0 0 1 0 0 0 0 0
## sample_CTTGA_Div6 0 0 1 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 1 NA NA NA 0 0
## sample_GTATT_Div10 0 0 1 1 0 NA 0 0
## sample_GTATT_Div7 0 0 1 0 0 0 0 0
## sample_TGACCA_Div5 0 0 1 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 1 0 0 0 0 0
## [,174] [,175] [,176] [,177] [,178] [,179] [,180] [,181]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 1 0 0 0 0
## sample_CTAGC_Nel7 1 1 1 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 1 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 1 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Alt12 0 0 0 1 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA NA NA 0
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 1 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 NA NA 0 NA
## sample_CTTGCTT_Sub14 0 0 0 0 NA NA NA 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 1 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 1 0
## sample_GTATT_Sub12 0 0 0 0 NA NA NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 NA 0
## sample_ACAGTG_Cau2 0 0 0 0 NA NA NA 0
## sample_ACAGTG_Cau3 0 0 0 0 NA NA 0 1
## sample_ACTAT_Cau11 0 0 0 NA 1 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 NA 0 0 0
## sample_AGCCC_Cau7 0 0 0 NA 1 1 0 0
## sample_ATGAAAC_Cau12 0 0 0 NA 1 1 NA 0
## sample_CTAGC_Cau5 0 0 0 0 1 1 0 0
## sample_CTGTA_Cau8 0 0 0 NA NA 1 NA 0
## sample_GGACCTA_Cau13 0 0 0 0 1 1 0 0
## sample_TCACC_Cau1 0 0 0 0 1 1 0 0
## sample_TCACC_Cau4 0 0 0 NA NA NA 0 0
## sample_TGACCA_Cau6 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 1 1 NA 0
## sample_AAAAGTT_Div13 0 0 0 0 1 0 NA 0
## sample_ACTAT_Div14 0 0 0 0 NA 1 0 0
## sample_AGCAT_Div11 0 0 0 0 NA 1 NA 0
## sample_AGCCC_Div9 0 0 0 0 1 1 0 0
## sample_ATCACG_Div1 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 NA 0 0 0
## sample_CGATGT_Div3 0 0 0 0 1 0 0 0
## sample_CTAGC_Div2 0 0 0 0 1 0 0 0
## sample_CTTGA_Div6 0 0 0 0 1 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 NA 1 NA 0
## sample_GTATT_Div10 0 0 0 0 1 NA NA 0
## sample_GTATT_Div7 0 0 0 0 NA 1 NA 0
## sample_TGACCA_Div5 0 0 0 0 NA 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 1 0 0 0
## [,182] [,183] [,184] [,185] [,186] [,187] [,188] [,189]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 1
## sample_ACAGTG_Nel5 0 1 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 1
## sample_CGATGT_Nel4 0 1 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 1 0 0 0
## sample_CTGTA_Nel9 0 0 0 1 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 1 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 1 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 1 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 0 0 0 NA
## sample_ACAAA_Sub1 NA 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 NA NA NA 0
## sample_CGATGT_Sub6 NA 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 NA NA NA 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 NA NA NA 0
## sample_ACAGTG_Cau3 0 0 0 0 0 1 1 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 1 0
## sample_ACTAT_Cau9 0 0 0 0 0 1 1 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 1 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 1 0
## sample_CTGTA_Cau8 0 0 0 0 NA NA NA 0
## sample_GGACCTA_Cau13 0 0 0 0 NA NA NA 0
## sample_TCACC_Cau1 0 0 0 0 0 0 1 0
## sample_TCACC_Cau4 0 0 0 0 0 0 1 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 1 0
## sample_ACTAT_Div14 0 0 0 0 0 1 1 0
## sample_AGCAT_Div11 0 0 1 0 0 0 1 0
## sample_AGCCC_Div9 0 0 0 0 0 0 1 0
## sample_ATCACG_Div1 0 0 1 0 0 0 1 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 1 0
## sample_CGATGT_Div3 0 0 0 0 0 1 1 0
## sample_CTAGC_Div2 0 0 0 0 0 0 1 0
## sample_CTTGA_Div6 0 0 0 0 0 1 1 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 1 0
## sample_GTATT_Div10 0 0 0 0 0 0 1 0
## sample_GTATT_Div7 0 0 0 0 0 1 1 0
## sample_TGACCA_Div5 0 0 0 0 0 0 1 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 1 0
## [,190] [,191] [,192] [,193] [,194] [,195] [,196] [,197]
## sample_ACAAA_Nel3 0 0 0 0 0 1 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 NA 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 1 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 NA 0 1 0
## sample_GGACCTA_Nel13 0 0 0 0 NA 0 1 0
## sample_GTATT_Nel14 0 0 0 0 0 0 1 0
## sample_TCACC_Nel6 0 0 0 0 NA 1 1 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 1 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 1 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 NA 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 1 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA NA 0 0
## sample_ACAAA_Sub1 0 NA NA 0 0 NA 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 1 0 1 0 0
## sample_AGCCC_Sub11 0 0 1 0 NA 1 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 NA 0 NA NA 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 NA NA NA 0
## sample_TGACCA_Sub2 0 0 0 0 NA 1 1 0
## sample_ACAGTG_Cau2 1 0 1 0 NA 0 0 0
## sample_ACAGTG_Cau3 1 0 1 0 1 0 0 0
## sample_ACTAT_Cau11 1 0 1 0 1 0 0 0
## sample_ACTAT_Cau9 1 0 1 0 1 0 0 0
## sample_AGCCC_Cau7 1 0 1 0 1 0 0 0
## sample_ATGAAAC_Cau12 1 0 1 0 NA 0 0 0
## sample_CTAGC_Cau5 1 0 1 0 1 0 0 0
## sample_CTGTA_Cau8 1 0 1 0 1 0 0 0
## sample_GGACCTA_Cau13 1 0 0 0 1 0 0 0
## sample_TCACC_Cau1 1 0 1 0 1 0 0 0
## sample_TCACC_Cau4 1 0 1 0 1 0 0 0
## sample_TGACCA_Cau6 1 0 1 0 1 0 0 0
## sample_AAAAGTT_Div12 1 0 1 0 1 0 0 0
## sample_AAAAGTT_Div13 1 0 1 0 1 0 0 0
## sample_ACTAT_Div14 1 0 1 0 1 0 0 0
## sample_AGCAT_Div11 1 0 1 0 NA 0 0 1
## sample_AGCCC_Div9 1 0 1 0 1 0 0 0
## sample_ATCACG_Div1 1 0 1 0 1 0 0 0
## sample_ATGAAAC_Div8 1 0 1 0 NA 0 0 0
## sample_CGATGT_Div3 1 0 1 0 1 0 0 0
## sample_CTAGC_Div2 1 1 1 0 1 0 0 0
## sample_CTTGA_Div6 1 0 1 0 1 0 0 0
## sample_CTTGCTT_Div15 1 NA NA 0 NA NA 0 0
## sample_GTATT_Div10 1 0 1 0 NA 0 0 0
## sample_GTATT_Div7 1 0 1 0 NA 0 0 0
## sample_TGACCA_Div5 1 0 1 0 1 0 0 0
## sample_TTAGGC_Div4 1 0 1 0 1 0 0 0
## [,198] [,199] [,200] [,201] [,202] [,203] [,204] [,205]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 1 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 1
## sample_GGACCTA_Nel13 0 1 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 1
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 NA
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 1
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 1 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 1 0 0
## sample_GCCAAT_Alt9 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 1 1 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA 0 0 NA 0
## sample_ACAAA_Sub1 0 0 0 0 0 0 NA 0
## sample_ACTAT_Sub7 0 0 0 1 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 NA
## sample_CGATGT_Sub6 NA NA NA 0 0 0 0 1
## sample_CTTGCTT_Sub14 NA NA NA 0 0 0 NA 0
## sample_GAATTCA_Sub9 0 0 0 1 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA NA NA 0 0 NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA NA NA 0 0 0 0 0
## sample_ACAGTG_Cau3 NA NA NA 0 0 0 1 0
## sample_ACTAT_Cau11 0 1 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 1 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 NA NA NA 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 NA NA NA NA 0 0 NA 0
## sample_GGACCTA_Cau13 NA NA NA 0 0 0 NA 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 NA 0
## sample_TGACCA_Cau6 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 1 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 1 0 0 0 0 0 0
## sample_ATCACG_Div1 0 1 0 0 0 0 NA 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 1 0 0 0 0 NA 0
## sample_CTAGC_Div2 0 0 0 0 0 0 NA 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 NA NA NA 0 0 0 NA 0
## sample_GTATT_Div10 0 1 0 0 0 0 0 0
## sample_GTATT_Div7 0 1 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 1 0 0 0 0 0 0
## [,206] [,207] [,208] [,209] [,210] [,211] [,212] [,213]
## sample_ACAAA_Nel3 0 0 1 0 0 0 1 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 1 1
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 1 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 1 0
## sample_GTATT_Nel14 0 0 0 0 0 0 1 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 1 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 1 1 0 0 1 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 1 0 0 1 1 0
## sample_CTGTA_Alt14 1 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 1 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 1 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Sub15 NA NA 0 0 0 0 0 0
## sample_ACAAA_Sub1 0 0 0 0 0 0 1 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 1 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 1 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 1 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 1 0
## sample_GTATT_Sub12 NA NA NA NA NA NA 0 1
## sample_TGACCA_Sub2 0 0 1 0 0 0 1 NA
## sample_ACAGTG_Cau2 0 0 0 1 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 1 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 1 0 0 1 0
## sample_ACTAT_Cau9 0 0 0 1 0 0 1 0
## sample_AGCCC_Cau7 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 1 0 0 NA 0
## sample_CTAGC_Cau5 0 0 0 1 0 0 1 0
## sample_CTGTA_Cau8 0 0 NA NA NA NA 0 0
## sample_GGACCTA_Cau13 0 0 0 1 0 0 1 0
## sample_TCACC_Cau1 0 0 0 1 0 0 1 0
## sample_TCACC_Cau4 0 0 0 1 0 0 1 0
## sample_TGACCA_Cau6 0 0 0 1 0 0 1 0
## sample_AAAAGTT_Div12 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 1 1 0 1 0
## sample_ACTAT_Div14 0 0 0 1 0 0 0 0
## sample_AGCAT_Div11 0 0 0 1 0 0 1 0
## sample_AGCCC_Div9 0 0 0 1 0 0 0 0
## sample_ATCACG_Div1 0 0 0 1 0 0 1 0
## sample_ATGAAAC_Div8 0 0 0 1 0 0 0 0
## sample_CGATGT_Div3 0 0 0 1 0 0 0 0
## sample_CTAGC_Div2 0 0 0 1 0 0 1 0
## sample_CTTGA_Div6 0 0 0 1 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 1 0 0 0 0
## sample_GTATT_Div10 0 0 0 1 0 0 1 0
## sample_GTATT_Div7 0 0 0 1 0 0 1 0
## sample_TGACCA_Div5 0 0 0 1 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 1 0 0 0 0
## [,214] [,215] [,216] [,217] [,218] [,219] [,220] [,221]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 1 1 0 0 0 0 0 1
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 1 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 1 1 0 0 0 0 0 0
## sample_CTGTA_Nel9 1 1 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 1 1 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 1 1 0 1 0 0 0 0
## sample_TGACCA_Nel1 1 1 0 0 0 0 0 1
## sample_AAAAGTT_Alt12 1 1 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 1 1 0 0 0 0 0 0
## sample_ATCACG_Alt5 NA NA NA 0 0 NA NA 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 1 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 1
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 1 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 1 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 0 NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 1 1 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 1 1 0 0 0 0 0 NA
## sample_CTTGCTT_Sub14 NA NA NA 0 0 NA NA 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 NA NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 NA 0 0 1
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 1
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 1
## sample_ACTAT_Cau9 0 0 1 0 0 0 0 1
## sample_AGCCC_Cau7 0 0 0 0 NA 0 0 1
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 0 1
## sample_CTAGC_Cau5 0 0 0 0 1 0 0 1
## sample_CTGTA_Cau8 0 0 0 0 0 NA NA 1
## sample_GGACCTA_Cau13 0 0 0 0 0 NA NA 0
## sample_TCACC_Cau1 0 0 0 0 1 0 0 1
## sample_TCACC_Cau4 0 0 0 0 NA 1 0 1
## sample_TGACCA_Cau6 0 0 0 0 1 0 0 1
## sample_AAAAGTT_Div12 0 0 0 0 1 1 0 1
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 1
## sample_ACTAT_Div14 0 0 0 0 0 0 0 1
## sample_AGCAT_Div11 0 0 0 0 1 NA NA 1
## sample_AGCCC_Div9 0 0 0 0 0 0 0 1
## sample_ATCACG_Div1 0 0 0 0 1 0 0 1
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 1
## sample_CGATGT_Div3 0 0 0 0 1 0 0 1
## sample_CTAGC_Div2 0 0 0 0 1 0 0 1
## sample_CTTGA_Div6 0 0 0 0 0 0 0 1
## sample_CTTGCTT_Div15 0 0 1 0 0 NA NA 1
## sample_GTATT_Div10 0 0 0 0 1 0 0 1
## sample_GTATT_Div7 0 0 0 0 0 0 0 NA
## sample_TGACCA_Div5 0 0 0 0 0 1 0 1
## sample_TTAGGC_Div4 0 0 1 0 0 0 0 1
## [,222] [,223] [,224] [,225] [,226] [,227] [,228] [,229]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 1 0 1 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 1 0 0 0
## sample_CGATGT_Nel4 0 0 1 0 0 0 0 0
## sample_CTAGC_Nel7 0 1 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 1
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 1 0 1 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 1 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 1 0 0 0 0 0
## sample_TGACCA_Nel1 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 1 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 1 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA 0 0 NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 0 NA NA
## sample_ACTAT_Sub7 0 0 1 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 1 0 0 0 0 0
## sample_CGATGT_Sub6 NA 0 0 0 0 0 NA NA
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 1 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 1 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 0 NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 1
## sample_ACAGTG_Cau2 0 0 0 0 0 0 NA NA
## sample_ACAGTG_Cau3 0 0 0 0 0 0 1 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 NA NA
## sample_ACTAT_Cau9 0 0 0 0 0 0 1 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Cau12 0 0 0 1 NA 0 NA NA
## sample_CTAGC_Cau5 0 0 0 0 0 0 1 0
## sample_CTGTA_Cau8 0 0 0 0 0 0 1 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 1 0
## sample_TCACC_Cau1 0 0 0 0 0 0 1 0
## sample_TCACC_Cau4 0 0 0 0 NA 0 NA NA
## sample_TGACCA_Cau6 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 1 0
## sample_ACTAT_Div14 0 0 0 0 0 0 1 0
## sample_AGCAT_Div11 0 0 0 0 0 0 NA NA
## sample_AGCCC_Div9 0 0 0 0 0 0 1 0
## sample_ATCACG_Div1 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Div8 0 NA NA NA 0 0 NA NA
## sample_CGATGT_Div3 0 0 0 0 0 0 1 0
## sample_CTAGC_Div2 0 0 0 0 0 0 NA 0
## sample_CTTGA_Div6 0 0 0 0 0 0 1 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 NA NA
## sample_GTATT_Div10 0 0 0 0 0 0 NA NA
## sample_GTATT_Div7 NA NA NA NA NA 1 NA NA
## sample_TGACCA_Div5 0 0 0 0 0 0 1 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 1 0
## [,230] [,231] [,232] [,233] [,234] [,235] [,236] [,237]
## sample_ACAAA_Nel3 0 0 0 0 0 1 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 1 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 1 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 1 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 1 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 1 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 1 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 1 0
## sample_TCACC_Nel6 0 0 0 0 0 1 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 1 0 1 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 1 1 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 1 0 0 1 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 1 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA 0 NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 1 0 0
## sample_ACTAT_Sub7 0 0 1 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 1 0 0
## sample_CGATGT_Sub6 0 NA 0 0 0 1 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 1 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 1 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 0 NA 0
## sample_TGACCA_Sub2 0 0 1 0 0 1 0 0
## sample_ACAGTG_Cau2 NA 0 0 0 0 0 0 1
## sample_ACAGTG_Cau3 NA 0 0 0 0 0 0 1
## sample_ACTAT_Cau11 1 1 0 0 0 0 0 1
## sample_ACTAT_Cau9 1 0 0 0 0 0 0 1
## sample_AGCCC_Cau7 NA 0 0 0 0 0 0 1
## sample_ATGAAAC_Cau12 NA NA 0 0 0 0 0 1
## sample_CTAGC_Cau5 1 0 0 0 0 0 0 1
## sample_CTGTA_Cau8 NA NA 0 0 0 0 NA 1
## sample_GGACCTA_Cau13 1 0 0 0 0 0 0 NA
## sample_TCACC_Cau1 1 0 0 0 0 0 0 1
## sample_TCACC_Cau4 NA 0 0 0 0 0 0 1
## sample_TGACCA_Cau6 1 0 0 0 0 0 0 1
## sample_AAAAGTT_Div12 1 0 0 0 0 0 0 1
## sample_AAAAGTT_Div13 1 0 0 0 0 0 0 1
## sample_ACTAT_Div14 1 0 0 0 0 0 0 1
## sample_AGCAT_Div11 1 1 0 0 0 0 0 1
## sample_AGCCC_Div9 1 1 0 0 0 0 0 1
## sample_ATCACG_Div1 1 0 0 0 0 0 0 1
## sample_ATGAAAC_Div8 1 0 0 0 0 0 0 1
## sample_CGATGT_Div3 1 0 0 0 0 0 0 1
## sample_CTAGC_Div2 1 1 0 0 0 0 0 1
## sample_CTTGA_Div6 1 0 0 0 0 0 0 1
## sample_CTTGCTT_Div15 NA NA 0 0 0 0 0 1
## sample_GTATT_Div10 1 1 0 0 0 0 0 1
## sample_GTATT_Div7 1 0 0 0 0 0 0 1
## sample_TGACCA_Div5 1 0 0 0 0 0 0 1
## sample_TTAGGC_Div4 1 1 0 0 0 0 0 1
## [,238] [,239] [,240] [,241] [,242] [,243] [,244] [,245]
## sample_ACAAA_Nel3 0 0 0 0 0 1 0 1
## sample_ACAGTG_Nel5 0 0 0 0 1 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 1 1 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 1 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 1 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 1 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 1 1 0 1
## sample_AAAAGTT_Alt12 0 0 0 0 0 1 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 1 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 1 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 1 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 1 0 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA 1 NA 0
## sample_ACAAA_Sub1 NA NA NA NA NA 1 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 1 0 1
## sample_AGCAT_Sub13 0 0 0 0 0 1 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 1 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 1 0 0
## sample_CTTGCTT_Sub14 NA NA NA 0 0 1 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 1 0 0
## sample_GTATT_Sub12 NA NA NA 0 0 NA 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 1 0 0
## sample_ACAGTG_Cau2 0 NA NA 1 0 NA 1 NA
## sample_ACAGTG_Cau3 0 NA NA 1 0 0 1 0
## sample_ACTAT_Cau11 0 0 0 1 0 0 1 0
## sample_ACTAT_Cau9 0 0 0 1 0 0 1 0
## sample_AGCCC_Cau7 0 0 1 NA NA 0 1 0
## sample_ATGAAAC_Cau12 0 NA NA NA NA 0 1 NA
## sample_CTAGC_Cau5 0 0 0 0 0 0 1 0
## sample_CTGTA_Cau8 0 0 1 1 0 0 1 0
## sample_GGACCTA_Cau13 0 NA NA 1 0 0 1 0
## sample_TCACC_Cau1 0 0 0 1 0 0 1 0
## sample_TCACC_Cau4 0 0 0 1 0 0 1 0
## sample_TGACCA_Cau6 0 0 1 1 0 0 1 0
## sample_AAAAGTT_Div12 0 NA NA 1 0 0 1 0
## sample_AAAAGTT_Div13 0 NA NA 1 0 0 1 0
## sample_ACTAT_Div14 0 0 1 1 0 0 1 0
## sample_AGCAT_Div11 0 NA NA 1 0 0 1 0
## sample_AGCCC_Div9 0 NA NA 1 0 0 1 0
## sample_ATCACG_Div1 0 0 0 1 0 0 1 0
## sample_ATGAAAC_Div8 0 0 0 1 0 0 1 0
## sample_CGATGT_Div3 0 1 0 1 0 0 1 0
## sample_CTAGC_Div2 0 0 0 1 0 0 1 0
## sample_CTTGA_Div6 0 0 0 0 0 0 1 0
## sample_CTTGCTT_Div15 0 NA NA 1 0 0 1 0
## sample_GTATT_Div10 0 0 0 1 0 0 1 0
## sample_GTATT_Div7 NA 1 0 1 0 0 1 0
## sample_TGACCA_Div5 0 NA NA 1 0 0 1 0
## sample_TTAGGC_Div4 0 0 0 1 0 0 1 0
## [,246] [,247] [,248] [,249] [,250] [,251] [,252] [,253]
## sample_ACAAA_Nel3 0 0 0 0 1 0 0 1
## sample_ACAGTG_Nel5 0 0 0 0 1 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 NA 1 0 0 0
## sample_CGATGT_Nel4 0 0 0 NA 1 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 1 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 1 0 0 1
## sample_CTGTA_Nel9 1 1 0 0 1 0 0 1
## sample_CTTGA_Nel2 0 0 0 0 1 0 0 1
## sample_GGACCTA_Nel11 0 0 0 1 1 0 0 1
## sample_GGACCTA_Nel13 0 0 0 0 0 1 0 1
## sample_GTATT_Nel14 0 0 0 NA 1 0 0 1
## sample_TCACC_Nel6 0 0 0 NA 1 0 0 1
## sample_TGACCA_Nel1 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 1 0 0 1
## sample_ACAGTG_Alt3 0 0 0 0 NA NA 0 0
## sample_AGCCC_Alt13 0 0 0 NA 1 0 0 0
## sample_ATCACG_Alt5 0 0 0 NA 1 0 0 1
## sample_ATCACG_Alt7 0 0 0 0 1 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 1 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 1 0 0 0
## sample_CTTGA_Alt10 0 0 0 NA 1 0 0 1
## sample_GAATTCA_Alt15 0 0 0 0 1 0 0 1
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 1
## sample_GCCAAT_Alt9 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 1 0 0 1
## sample_TTAGGC_Alt6 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 1 0 0 1
## sample_AAAAGTT_Sub15 NA NA NA NA 0 1 NA NA
## sample_ACAAA_Sub1 0 0 NA 0 NA NA NA NA
## sample_ACTAT_Sub7 0 0 0 0 1 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 1 0 0 0
## sample_AGCCC_Sub11 1 1 1 NA 0 1 NA NA
## sample_CGATGT_Sub6 0 0 NA NA NA NA NA NA
## sample_CTTGCTT_Sub14 1 1 NA NA 1 0 NA NA
## sample_GAATTCA_Sub9 0 0 1 0 1 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 1 0 0 1
## sample_GTATT_Sub12 NA NA 0 NA NA NA 0 1
## sample_TGACCA_Sub2 0 0 0 0 NA NA 0 1
## sample_ACAGTG_Cau2 0 0 NA 0 NA NA 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 1 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 1 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Cau12 0 0 0 NA 0 1 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 1 0 0
## sample_CTGTA_Cau8 0 0 0 0 NA NA NA NA
## sample_GGACCTA_Cau13 0 0 0 0 NA NA 0 0
## sample_TCACC_Cau1 0 0 0 0 0 1 0 0
## sample_TCACC_Cau4 0 0 0 NA 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 NA 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 NA NA 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 1 0 0
## sample_AGCAT_Div11 0 0 0 0 NA NA 0 0
## sample_AGCCC_Div9 0 0 0 0 0 1 0 0
## sample_ATCACG_Div1 0 0 0 0 NA NA 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 1 0 0
## sample_CGATGT_Div3 0 0 0 0 0 1 0 0
## sample_CTAGC_Div2 0 0 0 0 0 1 1 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 NA NA 0 0
## sample_GTATT_Div10 0 0 0 0 0 1 0 0
## sample_GTATT_Div7 0 0 0 0 NA NA 1 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 1 0 0
## [,254] [,255] [,256] [,257] [,258] [,259] [,260] [,261]
## sample_ACAAA_Nel3 0 1 0 0 1 0 0 0
## sample_ACAGTG_Nel5 0 1 0 0 1 0 0 0
## sample_AGCAT_Nel8 0 1 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel15 0 1 0 0 1 0 0 0
## sample_CGATGT_Nel4 0 0 0 1 1 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 NA NA 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 1 0 1 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 1 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 1 0 0 0
## sample_GGACCTA_Nel13 0 1 0 0 1 0 0 0
## sample_GTATT_Nel14 0 1 0 1 1 0 0 0
## sample_TCACC_Nel6 0 1 0 1 1 0 0 0
## sample_TGACCA_Nel1 0 1 0 0 1 0 0 0
## sample_AAAAGTT_Alt12 0 1 1 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 1 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 1 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 1 0 0 0
## sample_ATCACG_Alt5 0 1 0 1 1 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 1 1 0 1 0 0 0
## sample_CTTGA_Alt10 0 1 0 0 1 0 0 0
## sample_GAATTCA_Alt15 0 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt8 0 0 0 1 1 0 0 0
## sample_AAAAGTT_Sub15 0 NA 0 0 1 0 0 NA
## sample_ACAAA_Sub1 0 0 1 0 NA NA 0 NA
## sample_ACTAT_Sub7 0 0 1 0 1 0 1 0
## sample_AGCAT_Sub13 0 0 0 0 1 0 0 0
## sample_AGCCC_Sub11 NA NA 0 0 1 0 NA 0
## sample_CGATGT_Sub6 0 0 NA 0 1 0 0 0
## sample_CTTGCTT_Sub14 NA 0 NA 0 NA NA 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 1 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 1 0 0 0
## sample_GTATT_Sub12 NA NA NA 0 0 0 NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 NA 0
## sample_ACAGTG_Cau2 0 0 NA 0 0 0 NA 1
## sample_ACAGTG_Cau3 0 0 0 0 0 1 1 0
## sample_ACTAT_Cau11 0 0 0 0 0 1 1 1
## sample_ACTAT_Cau9 0 0 0 0 0 1 1 1
## sample_AGCCC_Cau7 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Cau12 0 0 0 0 NA NA NA 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 1 1
## sample_CTGTA_Cau8 NA 0 0 0 0 1 NA NA
## sample_GGACCTA_Cau13 0 0 0 0 0 0 1 NA
## sample_TCACC_Cau1 0 0 0 0 0 0 1 1
## sample_TCACC_Cau4 0 0 0 0 NA NA NA NA
## sample_TGACCA_Cau6 0 0 0 0 0 1 1 1
## sample_AAAAGTT_Div12 0 0 0 0 0 0 1 1
## sample_AAAAGTT_Div13 0 0 0 0 0 0 NA 1
## sample_ACTAT_Div14 0 0 0 0 0 0 1 1
## sample_AGCAT_Div11 0 0 NA 0 0 1 NA 1
## sample_AGCCC_Div9 0 0 0 0 0 0 1 1
## sample_ATCACG_Div1 0 0 0 0 0 1 1 1
## sample_ATGAAAC_Div8 0 0 0 0 0 1 1 1
## sample_CGATGT_Div3 0 0 0 0 0 0 1 1
## sample_CTAGC_Div2 0 0 0 0 0 0 NA 1
## sample_CTTGA_Div6 0 0 0 0 0 1 1 0
## sample_CTTGCTT_Div15 0 0 0 0 0 1 NA 1
## sample_GTATT_Div10 0 0 NA 0 0 0 NA 0
## sample_GTATT_Div7 0 0 0 0 0 0 NA 0
## sample_TGACCA_Div5 1 0 0 0 0 0 1 1
## sample_TTAGGC_Div4 0 0 0 0 0 1 1 1
## [,262] [,263] [,264] [,265] [,266] [,267] [,268] [,269]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 1 1 0 0 1 0 1 0
## sample_AGCAT_Nel8 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 1 1 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 1 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 1 0 0 0
## sample_CTTGA_Nel2 1 0 0 0 0 0 1 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 1 0 0 0 1 0 0 1
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 1 0 0 0 1 0 0 0
## sample_ATCACG_Alt5 0 0 0 1 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 1 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 1 0 1 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt2 1 0 0 0 1 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 NA NA NA 0 0 NA
## sample_ACAAA_Sub1 0 0 0 NA 1 0 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 NA 0 1 0 0 0
## sample_CGATGT_Sub6 NA NA 0 0 0 NA 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 1 0 0 NA
## sample_GAATTCA_Sub9 1 0 0 0 1 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 1 1 0 0
## sample_GTATT_Sub12 0 0 0 NA 1 0 NA 0
## sample_TGACCA_Sub2 0 0 0 0 1 0 0 NA
## sample_ACAGTG_Cau2 1 0 1 0 1 1 NA 0
## sample_ACAGTG_Cau3 1 0 1 0 1 1 0 0
## sample_ACTAT_Cau11 1 0 1 0 1 1 0 0
## sample_ACTAT_Cau9 1 0 1 0 1 1 0 0
## sample_AGCCC_Cau7 1 0 1 0 1 1 0 0
## sample_ATGAAAC_Cau12 1 0 1 NA 1 1 0 NA
## sample_CTAGC_Cau5 1 0 1 0 1 1 0 0
## sample_CTGTA_Cau8 1 0 NA NA 1 1 0 0
## sample_GGACCTA_Cau13 1 0 1 0 1 1 0 NA
## sample_TCACC_Cau1 1 0 1 0 1 1 0 0
## sample_TCACC_Cau4 1 0 1 0 1 1 0 0
## sample_TGACCA_Cau6 1 0 1 0 1 1 0 0
## sample_AAAAGTT_Div12 1 0 1 0 1 1 0 0
## sample_AAAAGTT_Div13 1 0 1 0 1 1 0 0
## sample_ACTAT_Div14 1 0 1 0 1 1 0 0
## sample_AGCAT_Div11 NA NA 1 0 1 1 0 NA
## sample_AGCCC_Div9 1 0 1 0 1 1 0 0
## sample_ATCACG_Div1 1 0 0 0 1 1 0 0
## sample_ATGAAAC_Div8 1 0 1 0 1 1 0 0
## sample_CGATGT_Div3 1 0 0 0 1 0 0 0
## sample_CTAGC_Div2 1 0 1 0 1 1 0 0
## sample_CTTGA_Div6 1 0 1 0 1 1 0 0
## sample_CTTGCTT_Div15 1 0 1 0 1 1 0 NA
## sample_GTATT_Div10 1 0 1 0 1 1 0 0
## sample_GTATT_Div7 1 0 1 0 1 1 0 0
## sample_TGACCA_Div5 1 0 1 0 1 1 0 0
## sample_TTAGGC_Div4 1 0 0 0 1 1 0 0
## [,270] [,271] [,272] [,273] [,274] [,275] [,276] [,277]
## sample_ACAAA_Nel3 1 1 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 1 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 1 0 1 0 0 0 0 0
## sample_CTGTA_Nel12 1 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 1 0 0 NA 0 0 0 0
## sample_GGACCTA_Nel11 1 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 1 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 NA 0 0 0 0
## sample_AAAAGTT_Alt12 1 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 1 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 1 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 1 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 1 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 1 1 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 1
## sample_CTTGA_Alt10 1 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 1 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 1 1 0 0 0 0 0 0
## sample_TTAGGC_Alt6 1 1 1 0 0 0 0 0
## sample_TTAGGC_Alt8 1 1 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 1 NA NA 0 NA 0 0
## sample_ACAAA_Sub1 NA NA NA NA 0 1 0 0
## sample_ACTAT_Sub7 1 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 NA NA 0 0 0 0 0 0
## sample_CGATGT_Sub6 NA NA 0 0 0 NA 0 0
## sample_CTTGCTT_Sub14 0 0 NA NA 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 1 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA 0 NA 0 NA 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 NA 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 NA 0 0 1 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 NA 0 0 1 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 NA NA 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 NA 0 0 NA NA
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 1 0 0 1 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 NA 0 0 0 0
## sample_ACTAT_Div14 0 0 0 1 0 0 0 0
## sample_AGCAT_Div11 0 0 0 NA 0 0 1 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 1 0 0 0
## sample_CGATGT_Div3 0 0 0 1 0 0 0 0
## sample_CTAGC_Div2 0 0 0 NA 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 NA 0 0 0 NA NA
## sample_GTATT_Div10 0 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,278] [,279] [,280] [,281] [,282] [,283] [,284] [,285]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 1 1 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 1 1 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 1 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 1 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 1 0 0
## sample_GGACCTA_Nel13 0 0 0 0 1 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 1 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 1 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 1 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 1 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 1 0 0 0 1 1 0 0
## sample_GCCAAT_Alt4 1 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 1 0 0 1
## sample_TTAGGC_Alt6 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 NA 0 NA NA
## sample_ACAAA_Sub1 NA NA 0 0 NA 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 1 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 NA NA 0 0 1 0 0 0
## sample_CGATGT_Sub6 0 0 NA 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 NA 0 NA 0 NA 0
## sample_GAATTCA_Sub9 0 0 0 0 1 0 0 0
## sample_GGACCTA_Sub10 1 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA 0 0 NA 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 1 0 0 0
## sample_ACAGTG_Cau2 NA NA 0 0 0 0 0 NA
## sample_ACAGTG_Cau3 0 1 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 1 0 1 0 0 0 0
## sample_ACTAT_Cau9 0 1 0 0 0 0 0 0
## sample_AGCCC_Cau7 NA NA 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 NA NA 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 1 0 1 0 0 0 0
## sample_CTGTA_Cau8 NA NA NA 0 0 0 NA 0
## sample_GGACCTA_Cau13 0 1 0 1 NA 0 0 0
## sample_TCACC_Cau1 0 1 0 0 0 0 0 0
## sample_TCACC_Cau4 0 1 0 NA 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Div12 0 1 1 0 0 0 0 0
## sample_AAAAGTT_Div13 0 1 1 0 0 0 0 NA
## sample_ACTAT_Div14 0 1 0 1 0 0 0 NA
## sample_AGCAT_Div11 0 1 0 1 0 0 0 NA
## sample_AGCCC_Div9 0 1 0 0 0 0 0 0
## sample_ATCACG_Div1 0 1 0 0 0 0 0 0
## sample_ATGAAAC_Div8 NA NA 0 1 0 0 0 0
## sample_CGATGT_Div3 0 1 0 1 0 0 0 0
## sample_CTAGC_Div2 0 1 0 0 0 0 0 0
## sample_CTTGA_Div6 0 1 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 1 0 1 0 0 0 NA
## sample_GTATT_Div10 0 0 0 1 0 0 0 NA
## sample_GTATT_Div7 0 1 0 0 NA 0 0 0
## sample_TGACCA_Div5 0 1 0 1 0 0 0 0
## sample_TTAGGC_Div4 0 1 0 0 0 0 0 0
## [,286] [,287] [,288] [,289] [,290] [,291] [,292] [,293]
## sample_ACAAA_Nel3 0 1 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 1 0 0 1 0 0 0
## sample_AGCAT_Nel8 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 1 0 0 0 0 0 1
## sample_ATGAAAC_Nel15 0 0 1 0 0 0 0 0
## sample_CGATGT_Nel4 0 1 0 0 0 0 0 1
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 1 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 1 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 1 0 0 0 0 1 1
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 1 0 0
## sample_CTTGA_Alt10 0 0 1 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 NA NA NA 0 0 0
## sample_ACAAA_Sub1 0 0 1 1 0 0 0 1
## sample_ACTAT_Sub7 0 1 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 1 0 0 0 0 0
## sample_CGATGT_Sub6 NA NA 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 NA NA NA 0 0 0
## sample_GAATTCA_Sub9 0 1 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 1 0 0 0 0 0 0
## sample_GTATT_Sub12 0 1 NA NA NA NA NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 NA NA NA
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 0 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 NA NA NA 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 NA NA NA 0 0 0
## sample_GTATT_Div10 0 0 NA NA NA 0 0 0
## sample_GTATT_Div7 0 0 NA NA NA 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,294] [,295] [,296] [,297] [,298] [,299] [,300] [,301]
## sample_ACAAA_Nel3 0 0 1 0 0 0 1 0
## sample_ACAGTG_Nel5 0 0 1 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 1 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 1
## sample_CTGTA_Nel9 0 0 1 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 1 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 1 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 1 0 0 0 0 0
## sample_GTATT_Nel14 0 0 1 0 0 0 0 0
## sample_TCACC_Nel6 0 0 1 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0 1
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 1 0 NA 0 0 1
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 1 1 0 0 0 0
## sample_CGATGT_Alt1 0 0 1 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 1 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 1 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA 0 NA NA NA 0 0 0
## sample_ACAAA_Sub1 NA 0 NA 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 1 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 NA 0 NA NA 0 NA 0 NA
## sample_CTTGCTT_Sub14 0 0 NA 0 0 NA 0 0
## sample_GAATTCA_Sub9 0 0 1 0 0 NA 0 0
## sample_GGACCTA_Sub10 0 0 1 0 0 NA 0 0
## sample_GTATT_Sub12 NA 0 NA NA NA 0 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 NA 1 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 NA 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 1 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 1 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Cau12 0 1 0 0 1 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 1 0 0 0
## sample_CTGTA_Cau8 0 NA NA NA NA 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 1 0 0 0
## sample_TCACC_Cau1 0 0 0 0 1 0 0 0
## sample_TCACC_Cau4 0 0 0 0 1 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 1 1 0 0
## sample_AAAAGTT_Div13 0 0 0 0 1 0 0 0
## sample_ACTAT_Div14 0 1 0 0 1 0 0 0
## sample_AGCAT_Div11 0 1 0 0 1 0 0 0
## sample_AGCCC_Div9 1 0 0 0 1 0 0 0
## sample_ATCACG_Div1 0 1 0 0 1 0 0 0
## sample_ATGAAAC_Div8 0 1 0 NA 1 0 0 0
## sample_CGATGT_Div3 0 0 0 0 1 0 0 0
## sample_CTAGC_Div2 0 0 0 0 1 0 0 0
## sample_CTTGA_Div6 0 0 0 0 1 0 0 0
## sample_CTTGCTT_Div15 0 0 0 NA 1 0 0 0
## sample_GTATT_Div10 0 0 0 0 1 0 0 0
## sample_GTATT_Div7 0 0 0 NA 1 0 0 0
## sample_TGACCA_Div5 0 1 0 0 1 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 1 1 0 0
## [,302] [,303] [,304] [,305] [,306] [,307] [,308] [,309]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 1 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 1 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 NA NA NA NA NA
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 1 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Sub15 0 0 0 NA NA NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 1 1 0 0
## sample_ACTAT_Sub7 0 0 0 NA NA NA NA NA
## sample_AGCAT_Sub13 0 0 0 NA NA NA NA NA
## sample_AGCCC_Sub11 0 0 0 0 NA 1 0 0
## sample_CGATGT_Sub6 0 0 0 0 1 1 0 0
## sample_CTTGCTT_Sub14 NA NA 0 0 1 1 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 0 0 1 1 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA NA NA 0 1 1 0 0
## sample_ACAGTG_Cau3 1 0 0 0 1 1 1 1
## sample_ACTAT_Cau11 1 0 0 0 0 1 0 0
## sample_ACTAT_Cau9 1 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 1 0 0 0 1 1 0 0
## sample_ATGAAAC_Cau12 1 0 0 NA NA NA NA NA
## sample_CTAGC_Cau5 1 0 0 0 0 1 0 0
## sample_CTGTA_Cau8 1 0 0 NA NA NA NA NA
## sample_GGACCTA_Cau13 1 0 0 0 0 0 0 0
## sample_TCACC_Cau1 1 0 0 0 0 1 0 0
## sample_TCACC_Cau4 1 0 0 NA NA NA NA NA
## sample_TGACCA_Cau6 1 0 0 0 0 1 0 0
## sample_AAAAGTT_Div12 1 0 0 0 0 1 0 0
## sample_AAAAGTT_Div13 1 NA 0 0 0 1 0 0
## sample_ACTAT_Div14 1 0 0 0 1 1 1 1
## sample_AGCAT_Div11 1 NA 0 0 0 1 0 0
## sample_AGCCC_Div9 1 0 0 1 1 1 0 1
## sample_ATCACG_Div1 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 1 0 0 NA NA NA NA NA
## sample_CGATGT_Div3 1 0 0 0 0 1 0 0
## sample_CTAGC_Div2 1 0 0 0 0 0 0 0
## sample_CTTGA_Div6 1 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 1 NA 0 NA NA NA NA NA
## sample_GTATT_Div10 1 0 0 0 0 0 0 0
## sample_GTATT_Div7 1 0 0 0 0 1 0 0
## sample_TGACCA_Div5 NA 0 0 0 0 1 0 0
## sample_TTAGGC_Div4 1 0 0 0 0 0 0 0
## [,310] [,311] [,312] [,313] [,314] [,315] [,316] [,317]
## sample_ACAAA_Nel3 0 0 0 1 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 1 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 1 1 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 1 0 0 0
## sample_CGATGT_Nel4 0 0 0 1 0 0 1 0
## sample_CTAGC_Nel7 0 0 0 1 0 0 1 0
## sample_CTGTA_Nel12 0 0 0 1 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 1 1 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 1 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 1 0 0 1 0
## sample_GTATT_Nel14 0 0 1 1 0 0 0 0
## sample_TCACC_Nel6 0 0 1 1 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 1 1 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 1 0 0 0 0
## sample_ACAAA_Alt11 1 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 1 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 1 0 1 0
## sample_ATCACG_Alt5 NA 0 0 1 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 1 1 0 1 0
## sample_CGATGT_Alt1 0 0 1 1 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 1 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 1 0 0 1 0
## sample_GAATTCA_Alt15 0 0 0 1 1 0 0 0
## sample_GCCAAT_Alt4 0 0 0 1 1 0 0 1
## sample_GCCAAT_Alt9 0 0 0 1 0 0 0 1
## sample_TTAGGC_Alt2 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA NA NA NA
## sample_ACAAA_Sub1 0 0 NA NA 0 0 0 1
## sample_ACTAT_Sub7 NA 0 0 1 0 0 0 0
## sample_AGCAT_Sub13 NA 0 0 1 1 0 0 0
## sample_AGCCC_Sub11 0 0 NA NA 0 0 NA NA
## sample_CGATGT_Sub6 0 0 NA NA 0 0 NA NA
## sample_CTTGCTT_Sub14 0 NA 0 0 0 NA 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 1 0 0 0 0
## sample_GTATT_Sub12 0 NA 0 1 0 NA 0 0
## sample_TGACCA_Sub2 0 0 0 1 0 0 0 0
## sample_ACAGTG_Cau2 0 NA 0 0 0 NA NA 0
## sample_ACAGTG_Cau3 0 1 0 0 0 1 1 0
## sample_ACTAT_Cau11 0 1 0 0 0 0 1 0
## sample_ACTAT_Cau9 0 1 0 0 0 0 1 0
## sample_AGCCC_Cau7 0 1 0 0 0 0 1 0
## sample_ATGAAAC_Cau12 NA NA 0 0 0 0 1 0
## sample_CTAGC_Cau5 0 1 0 0 NA 0 1 0
## sample_CTGTA_Cau8 NA 1 0 0 0 0 1 0
## sample_GGACCTA_Cau13 0 1 NA NA 0 0 1 0
## sample_TCACC_Cau1 0 1 0 0 0 0 1 0
## sample_TCACC_Cau4 NA 1 0 0 0 1 1 0
## sample_TGACCA_Cau6 0 1 0 0 0 0 1 0
## sample_AAAAGTT_Div12 0 1 0 0 0 NA 1 0
## sample_AAAAGTT_Div13 0 NA 0 1 0 1 1 0
## sample_ACTAT_Div14 0 1 0 0 0 0 1 0
## sample_AGCAT_Div11 0 NA 0 0 0 0 1 0
## sample_AGCCC_Div9 0 1 0 0 0 0 1 0
## sample_ATCACG_Div1 0 1 0 0 0 0 1 0
## sample_ATGAAAC_Div8 NA 1 0 1 0 1 1 0
## sample_CGATGT_Div3 0 1 0 0 0 0 1 0
## sample_CTAGC_Div2 0 1 0 0 0 0 1 0
## sample_CTTGA_Div6 0 1 0 0 0 0 1 0
## sample_CTTGCTT_Div15 NA 1 0 0 NA NA 1 0
## sample_GTATT_Div10 0 1 0 0 0 NA 1 0
## sample_GTATT_Div7 0 NA 0 0 NA 0 1 0
## sample_TGACCA_Div5 0 1 0 0 0 0 1 0
## sample_TTAGGC_Div4 0 1 0 0 0 0 1 0
## [,318] [,319] [,320] [,321] [,322] [,323] [,324] [,325]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 1 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 1 1 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 1 0 0
## sample_GAATTCA_Alt15 0 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 1 0 0
## sample_GCCAAT_Alt9 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 1 0 0 0 1 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 1
## sample_AAAAGTT_Sub15 0 NA 0 0 0 1 0 NA
## sample_ACAAA_Sub1 0 0 0 0 0 NA 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 NA 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 1 0 0
## sample_CTTGCTT_Sub14 0 NA 0 0 0 NA 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 1 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 1 0 0
## sample_GTATT_Sub12 0 0 0 0 0 1 NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 NA 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 0 NA 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 NA 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 NA 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 NA 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 NA 0 0 0 0 NA 0
## sample_GGACCTA_Cau13 0 NA 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 1 0 1 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 NA 0
## sample_ACTAT_Div14 0 0 0 0 0 0 NA 0
## sample_AGCAT_Div11 0 0 0 0 0 0 NA 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 NA 0
## sample_GTATT_Div10 0 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 NA 0
## sample_TGACCA_Div5 0 0 0 0 0 0 NA 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,326] [,327] [,328] [,329] [,330] [,331] [,332] [,333]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 1 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 1 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 NA 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Sub15 NA NA 0 0 NA 0 0 0
## sample_ACAAA_Sub1 0 0 0 0 0 NA 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 NA 0 0 0
## sample_CTTGCTT_Sub14 NA NA 0 0 NA 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA 0 0 NA NA 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA 0 1 0 NA NA 0 0
## sample_ACAGTG_Cau3 0 0 1 0 0 0 0 0
## sample_ACTAT_Cau11 1 0 1 0 1 0 0 0
## sample_ACTAT_Cau9 0 0 1 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 NA 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 1 0 NA 0 0 0
## sample_CTAGC_Cau5 NA 0 1 0 0 0 0 0
## sample_CTGTA_Cau8 0 NA NA 0 NA NA 0 0
## sample_GGACCTA_Cau13 0 NA 1 0 NA 0 NA NA
## sample_TCACC_Cau1 0 0 NA 0 0 0 0 0
## sample_TCACC_Cau4 NA 0 1 0 NA 0 0 0
## sample_TGACCA_Cau6 0 0 NA 1 0 0 0 0
## sample_AAAAGTT_Div12 0 0 1 0 NA 0 0 0
## sample_AAAAGTT_Div13 NA 0 1 0 NA 0 0 0
## sample_ACTAT_Div14 0 0 1 0 0 0 1 0
## sample_AGCAT_Div11 NA 0 NA 0 NA 0 0 0
## sample_AGCCC_Div9 0 1 1 0 0 0 0 0
## sample_ATCACG_Div1 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 1 0 NA 0 0 0
## sample_CGATGT_Div3 0 0 1 0 0 0 0 0
## sample_CTAGC_Div2 0 1 1 0 0 0 0 0
## sample_CTTGA_Div6 0 0 1 0 1 0 0 0
## sample_CTTGCTT_Div15 0 0 NA 0 NA NA 0 0
## sample_GTATT_Div10 NA 0 1 0 NA 0 0 0
## sample_GTATT_Div7 NA 0 1 0 NA 0 0 0
## sample_TGACCA_Div5 0 0 NA 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 1 0 0 0 0 0
## [,334] [,335] [,336] [,337] [,338] [,339] [,340] [,341]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 1 0 1 0 0
## sample_AGCAT_Nel8 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 1 0 0
## sample_ATGAAAC_Nel15 0 0 1 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 1 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 1 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 1 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 1 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 1 0 0
## sample_AGCCC_Alt13 0 0 1 0 0 1 0 0
## sample_ATCACG_Alt5 0 0 0 1 0 0 0 0
## sample_ATCACG_Alt7 0 0 1 0 0 1 0 1
## sample_CGATGT_Alt1 0 0 0 0 0 1 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 1 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 1 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 1 0 0
## sample_GCCAAT_Alt9 0 0 1 0 0 1 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 1 0 1
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 NA 0 0 NA
## sample_ACAAA_Sub1 0 0 0 0 NA 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 1 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 NA 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 NA 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 NA 0 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 1 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 1 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 1 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 NA 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 0 NA 0 0 0
## sample_GGACCTA_Cau13 NA NA 0 0 NA 0 1 0
## sample_TCACC_Cau1 0 1 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 1 1 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 NA 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 1 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 1 0 0 0 0 1 0
## sample_CGATGT_Div3 0 1 0 0 0 0 0 0
## sample_CTAGC_Div2 0 1 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 NA 0 0 0
## sample_GTATT_Div10 0 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,342] [,343] [,344] [,345] [,346] [,347] [,348] [,349]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 1 0 0 0
## sample_AGCAT_Nel8 0 0 1 0 1 0 0 0
## sample_ATGAAAC_Nel10 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 1 0 1 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 1 1 0 0 0 0
## sample_CTGTA_Nel9 0 0 1 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 1 0 0 1 0
## sample_GGACCTA_Nel11 0 0 1 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 1 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 1 0 0 0 0
## sample_AGCCC_Alt13 0 0 1 1 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 1 0 0 0 0
## sample_ATCACG_Alt7 0 0 1 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 1 1 0 0 0 0
## sample_CTGTA_Alt14 0 0 1 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 1 1 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 1 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 1 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt2 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 1 0 NA NA 0
## sample_ACAAA_Sub1 0 NA NA 1 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 1 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 1 0 0 0 0
## sample_AGCCC_Sub11 0 NA NA 1 0 0 0 0
## sample_CGATGT_Sub6 0 NA NA 1 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 1 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 1 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 1 0 0 0 0
## sample_GTATT_Sub12 0 NA NA 1 0 0 NA 0
## sample_TGACCA_Sub2 0 0 0 1 0 0 NA 0
## sample_ACAGTG_Cau2 0 NA NA 0 0 0 NA 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 1
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 NA 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 0 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 NA 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 1 NA 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 1 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 NA 0
## sample_GTATT_Div10 0 NA NA 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,350] [,351] [,352] [,353] [,354] [,355] [,356] [,357]
## sample_ACAAA_Nel3 0 0 0 0 1 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 1
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 1 0 0 0 0 0 0 1
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 1 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 1 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 1 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 1
## sample_TCACC_Nel6 0 0 0 0 0 1 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 1 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 1 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 1 0 0 0
## sample_ATCACG_Alt5 1 0 0 0 1 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 1 0 0 1
## sample_CGATGT_Alt1 1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 1 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 1 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt2 1 0 0 0 1 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 NA NA 0 0 NA
## sample_ACAAA_Sub1 0 0 0 0 1 0 0 NA
## sample_ACTAT_Sub7 0 0 0 0 1 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 NA NA 0 0 NA
## sample_CGATGT_Sub6 1 0 0 0 1 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 NA NA NA NA 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 NA 0 1 0 0 NA
## sample_TGACCA_Sub2 0 0 0 0 1 NA NA 0
## sample_ACAGTG_Cau2 0 0 NA 1 0 0 0 0
## sample_ACAGTG_Cau3 0 0 1 1 0 0 1 0
## sample_ACTAT_Cau11 0 0 0 1 0 0 1 0
## sample_ACTAT_Cau9 0 0 0 1 0 0 1 0
## sample_AGCCC_Cau7 0 0 0 1 0 0 1 NA
## sample_ATGAAAC_Cau12 0 0 0 1 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 1 0 0 1 0
## sample_CTGTA_Cau8 0 0 0 1 0 0 1 0
## sample_GGACCTA_Cau13 0 0 0 1 0 NA NA 0
## sample_TCACC_Cau1 0 0 0 0 0 0 1 0
## sample_TCACC_Cau4 0 0 NA NA NA 0 0 0
## sample_TGACCA_Cau6 0 0 1 1 0 0 0 0
## sample_AAAAGTT_Div12 0 1 0 NA NA 0 1 0
## sample_AAAAGTT_Div13 0 0 0 1 0 0 0 0
## sample_ACTAT_Div14 0 0 1 1 0 0 1 0
## sample_AGCAT_Div11 0 0 0 NA NA NA NA 0
## sample_AGCCC_Div9 0 0 0 1 0 0 1 0
## sample_ATCACG_Div1 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Div8 0 0 0 1 0 0 1 0
## sample_CGATGT_Div3 0 0 0 1 0 0 1 0
## sample_CTAGC_Div2 0 0 0 1 0 0 1 0
## sample_CTTGA_Div6 0 0 1 1 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 NA NA 0
## sample_GTATT_Div10 0 0 0 0 0 NA NA 0
## sample_GTATT_Div7 0 0 0 1 0 NA NA 0
## sample_TGACCA_Div5 0 0 0 0 0 0 1 0
## sample_TTAGGC_Div4 0 0 0 1 0 0 1 0
## [,358] [,359] [,360] [,361] [,362] [,363] [,364] [,365]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 NA 0
## sample_CTTGA_Nel2 0 0 0 1 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 1 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 NA 0 NA NA NA 0
## sample_ACAAA_Sub1 0 0 NA 0 0 0 NA 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 NA 0 0 0 NA 0
## sample_CTTGCTT_Sub14 0 0 0 0 NA NA 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 NA 0 0 0 NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 1 0 0
## sample_ACAGTG_Cau2 0 0 NA 0 1 1 0 0
## sample_ACAGTG_Cau3 0 0 0 0 1 1 1 0
## sample_ACTAT_Cau11 0 0 0 0 1 1 NA 0
## sample_ACTAT_Cau9 0 0 0 0 1 1 1 0
## sample_AGCCC_Cau7 0 0 0 0 1 1 NA 0
## sample_ATGAAAC_Cau12 0 0 0 0 1 1 NA 0
## sample_CTAGC_Cau5 0 0 0 0 1 1 1 0
## sample_CTGTA_Cau8 0 0 NA 0 1 1 NA 0
## sample_GGACCTA_Cau13 0 0 0 0 1 1 1 0
## sample_TCACC_Cau1 0 0 0 0 1 1 1 0
## sample_TCACC_Cau4 0 0 0 0 1 1 NA 0
## sample_TGACCA_Cau6 0 0 0 0 1 1 1 0
## sample_AAAAGTT_Div12 0 0 0 0 1 1 NA 0
## sample_AAAAGTT_Div13 0 0 0 0 1 1 1 0
## sample_ACTAT_Div14 0 0 0 0 0 1 1 0
## sample_AGCAT_Div11 0 1 0 0 1 1 NA 0
## sample_AGCCC_Div9 1 0 0 0 1 1 1 0
## sample_ATCACG_Div1 0 0 0 0 1 1 NA 0
## sample_ATGAAAC_Div8 0 0 0 0 1 1 1 0
## sample_CGATGT_Div3 0 0 0 0 0 1 1 0
## sample_CTAGC_Div2 0 0 0 0 1 1 1 0
## sample_CTTGA_Div6 0 0 0 0 1 1 NA 0
## sample_CTTGCTT_Div15 0 0 0 0 1 1 NA 0
## sample_GTATT_Div10 0 0 0 0 1 1 1 0
## sample_GTATT_Div7 0 0 0 0 1 1 NA 0
## sample_TGACCA_Div5 0 0 0 0 0 1 NA 0
## sample_TTAGGC_Div4 0 0 0 0 1 1 1 0
## [,366] [,367] [,368] [,369] [,370] [,371] [,372] [,373]
## sample_ACAAA_Nel3 1 0 0 0 1 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 1 0
## sample_AGCAT_Nel8 0 0 0 0 1 0 1 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 1 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 1 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 1 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 1 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 1 0
## sample_TGACCA_Nel1 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 1 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 1 0 1 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 1 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 1 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 1 0 1 0
## sample_CTTGA_Alt10 0 0 0 0 1 0 0 0
## sample_GAATTCA_Alt15 0 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 NA NA NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 1 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 1 0 0 0
## sample_AGCCC_Sub11 NA NA 0 NA NA 0 0 0
## sample_CGATGT_Sub6 NA NA 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 NA NA NA 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA 0 NA NA 0 0 0
## sample_TGACCA_Sub2 NA NA 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 NA NA 0 0 0
## sample_ACAGTG_Cau3 NA NA 0 1 0 0 0 0
## sample_ACTAT_Cau11 0 0 1 1 0 0 0 0
## sample_ACTAT_Cau9 0 1 0 1 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 1 0 NA NA 0
## sample_CTAGC_Cau5 0 1 0 1 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 1 0 0 0 NA
## sample_GGACCTA_Cau13 NA NA 0 1 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 NA NA 0 0 0
## sample_TGACCA_Cau6 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Div12 0 1 0 NA NA 0 0 1
## sample_AAAAGTT_Div13 0 1 0 NA NA 0 0 0
## sample_ACTAT_Div14 0 0 0 1 0 0 0 0
## sample_AGCAT_Div11 0 0 0 NA NA 0 0 0
## sample_AGCCC_Div9 0 0 0 1 0 0 0 0
## sample_ATCACG_Div1 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 1 0 0 0 0
## sample_CGATGT_Div3 0 0 0 1 0 0 0 1
## sample_CTAGC_Div2 0 0 0 1 0 0 0 0
## sample_CTTGA_Div6 0 1 0 1 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 NA NA 0 0 0
## sample_GTATT_Div10 0 0 0 NA NA 0 0 0
## sample_GTATT_Div7 0 0 0 NA NA 0 0 0
## sample_TGACCA_Div5 0 0 0 1 0 0 0 0
## sample_TTAGGC_Div4 0 1 0 1 0 0 0 0
## [,374] [,375] [,376] [,377] [,378] [,379] [,380] [,381]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 1 0 0
## sample_ATGAAAC_Nel15 1 0 0 0 0 1 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 1 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 1 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 1 0 0 1 1 1 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 1 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 1 0 0
## sample_ACTAT_Sub7 0 0 0 1 0 1 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 1 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 1 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 NA NA NA NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 1 0 0
## sample_GTATT_Sub12 NA NA NA NA 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 1 0 0
## sample_ACAGTG_Cau2 NA NA NA 0 0 0 1 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 1 1
## sample_ACTAT_Cau11 0 1 1 0 0 0 1 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 1
## sample_AGCCC_Cau7 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Cau12 0 0 0 NA 0 0 1 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 1 0
## sample_CTGTA_Cau8 NA NA NA 0 0 0 1 0
## sample_GGACCTA_Cau13 NA NA NA 0 0 0 1 1
## sample_TCACC_Cau1 0 0 0 0 0 0 0 1
## sample_TCACC_Cau4 NA NA NA 0 0 0 0 1
## sample_TGACCA_Cau6 0 0 0 0 0 0 1 1
## sample_AAAAGTT_Div12 0 0 0 0 0 0 1 1
## sample_AAAAGTT_Div13 0 0 0 0 0 0 1 1
## sample_ACTAT_Div14 0 0 0 0 0 0 0 1
## sample_AGCAT_Div11 0 0 0 NA 0 0 1 1
## sample_AGCCC_Div9 0 0 0 0 0 0 1 0
## sample_ATCACG_Div1 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Div8 NA NA NA NA 0 0 1 0
## sample_CGATGT_Div3 0 1 1 NA 0 0 1 1
## sample_CTAGC_Div2 0 0 0 0 0 0 1 0
## sample_CTTGA_Div6 0 0 0 0 0 0 1 0
## sample_CTTGCTT_Div15 0 0 0 NA 0 0 1 1
## sample_GTATT_Div10 0 0 0 0 0 0 1 0
## sample_GTATT_Div7 NA NA NA NA 0 0 1 1
## sample_TGACCA_Div5 0 0 0 0 0 0 1 1
## sample_TTAGGC_Div4 0 0 0 0 0 0 1 0
## [,382] [,383] [,384] [,385] [,386] [,387] [,388] [,389]
## sample_ACAAA_Nel3 0 0 0 0 0 0 1 1
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 1
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 1
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 1
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 NA NA NA 0 0 0
## sample_CTGTA_Alt14 0 0 1 1 1 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 1
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 1 1 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 1
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 1 1 1
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA 0 NA NA NA 0 0 0
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 1
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 NA
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 NA 0 0 0 0 0 0
## sample_CGATGT_Sub6 NA 0 NA NA NA 0 0 0
## sample_CTTGCTT_Sub14 0 0 NA NA NA 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 0 0 0 0 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 1 NA 0 0 0 NA NA 0
## sample_ACAGTG_Cau3 NA 1 NA NA NA 0 0 0
## sample_ACTAT_Cau11 1 1 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 1 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 NA NA 0 0 0 0 0 0
## sample_CTAGC_Cau5 1 1 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 1 NA NA NA 0 0 0
## sample_GGACCTA_Cau13 0 1 0 0 0 0 0 0
## sample_TCACC_Cau1 0 1 0 0 0 0 0 0
## sample_TCACC_Cau4 0 NA 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Div12 1 1 0 0 0 0 0 0
## sample_AAAAGTT_Div13 1 1 0 0 0 0 0 0
## sample_ACTAT_Div14 0 1 0 0 0 0 0 0
## sample_AGCAT_Div11 0 1 0 0 0 0 0 0
## sample_AGCCC_Div9 0 NA 0 0 0 0 0 0
## sample_ATCACG_Div1 1 1 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 1 0 0 0 0 0 0
## sample_CGATGT_Div3 0 1 0 0 0 0 0 0
## sample_CTAGC_Div2 0 1 0 0 0 0 0 0
## sample_CTTGA_Div6 0 1 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 1 0 0 0 0 0 0
## sample_GTATT_Div10 1 1 0 0 0 0 0 0
## sample_GTATT_Div7 0 1 NA NA NA 0 0 0
## sample_TGACCA_Div5 1 1 0 0 0 0 0 0
## sample_TTAGGC_Div4 1 1 0 0 0 0 0 0
## [,390] [,391] [,392] [,393] [,394] [,395] [,396] [,397]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 1 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 1
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 1 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 1 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 1
## sample_ATCACG_Alt5 0 0 0 0 0 0 1 1
## sample_ATCACG_Alt7 0 0 0 0 0 0 1 1
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 1
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 1 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 1
## sample_TTAGGC_Alt6 0 1 0 1 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 0 NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 NA
## sample_ACTAT_Sub7 NA NA NA NA NA 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 0 NA
## sample_GAATTCA_Sub9 0 1 0 1 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA NA NA NA NA NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 1 0 1 0 1 0 0 1
## sample_ACAGTG_Cau3 1 0 1 0 1 1 0 1
## sample_ACTAT_Cau11 1 0 1 0 1 0 0 1
## sample_ACTAT_Cau9 1 0 1 0 1 0 0 1
## sample_AGCCC_Cau7 1 0 1 0 1 0 0 NA
## sample_ATGAAAC_Cau12 1 0 1 0 1 NA NA 1
## sample_CTAGC_Cau5 1 0 1 0 1 0 0 1
## sample_CTGTA_Cau8 1 0 1 0 1 NA NA 1
## sample_GGACCTA_Cau13 1 0 1 0 1 0 0 1
## sample_TCACC_Cau1 1 0 1 0 1 0 0 1
## sample_TCACC_Cau4 1 0 1 0 1 0 0 1
## sample_TGACCA_Cau6 1 0 1 0 1 0 0 1
## sample_AAAAGTT_Div12 1 0 1 0 1 0 0 1
## sample_AAAAGTT_Div13 1 0 1 0 1 0 0 1
## sample_ACTAT_Div14 1 0 1 0 1 0 0 1
## sample_AGCAT_Div11 1 0 1 0 1 0 0 1
## sample_AGCCC_Div9 1 0 1 0 1 0 0 1
## sample_ATCACG_Div1 1 0 1 0 1 0 0 1
## sample_ATGAAAC_Div8 1 0 1 0 1 0 0 1
## sample_CGATGT_Div3 1 0 1 0 1 0 0 1
## sample_CTAGC_Div2 1 0 1 0 1 0 0 1
## sample_CTTGA_Div6 1 0 1 0 1 0 0 1
## sample_CTTGCTT_Div15 1 0 1 0 1 0 0 1
## sample_GTATT_Div10 1 0 1 0 1 0 0 0
## sample_GTATT_Div7 1 0 1 0 1 0 0 1
## sample_TGACCA_Div5 1 0 1 0 1 0 0 1
## sample_TTAGGC_Div4 1 0 1 0 1 0 0 1
## [,398] [,399] [,400] [,401] [,402] [,403] [,404] [,405]
## sample_ACAAA_Nel3 1 0 0 0 1 1 0 1
## sample_ACAGTG_Nel5 1 0 0 0 0 1 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel15 1 0 0 1 1 1 0 0
## sample_CGATGT_Nel4 1 0 0 0 1 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 1 0 0
## sample_CTGTA_Nel12 0 1 0 0 0 1 0 0
## sample_CTGTA_Nel9 1 1 0 1 1 1 0 0
## sample_CTTGA_Nel2 0 0 0 0 1 0 0 0
## sample_GGACCTA_Nel11 0 1 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 1 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 1 0 0 0 1 1 0 0
## sample_TGACCA_Nel1 0 0 0 0 1 1 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 1 0 0
## sample_ACAAA_Alt11 0 0 0 0 1 1 0 0
## sample_ACAGTG_Alt3 1 0 0 0 1 1 0 0
## sample_AGCCC_Alt13 0 0 0 0 1 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 1 1 0 0
## sample_CGATGT_Alt1 0 1 0 0 1 0 0 0
## sample_CTGTA_Alt14 1 0 0 0 1 1 0 0
## sample_CTTGA_Alt10 0 0 0 0 1 1 0 0
## sample_GAATTCA_Alt15 0 0 1 0 0 1 0 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 1 1 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 1 1 0 0 0 1 0 0
## sample_TTAGGC_Alt8 1 1 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 NA 0 1 0 0
## sample_ACAAA_Sub1 NA 0 0 NA NA NA 0 0
## sample_ACTAT_Sub7 1 0 0 0 1 1 0 0
## sample_AGCAT_Sub13 1 1 0 0 1 1 0 0
## sample_AGCCC_Sub11 1 0 0 0 NA NA 0 0
## sample_CGATGT_Sub6 0 NA 0 0 1 0 0 0
## sample_CTTGCTT_Sub14 NA 0 0 0 NA 1 0 0
## sample_GAATTCA_Sub9 0 0 0 0 1 1 0 0
## sample_GGACCTA_Sub10 1 0 0 0 1 0 0 0
## sample_GTATT_Sub12 NA NA 0 NA NA 0 0 0
## sample_TGACCA_Sub2 1 NA 0 0 0 1 0 0
## sample_ACAGTG_Cau2 0 NA 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 NA 0 0 NA 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 1 0 0 0 0
## sample_CTGTA_Cau8 0 NA 0 NA 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 1 0 0 NA NA
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 1 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 1 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 1 0 0 NA NA
## sample_GTATT_Div10 0 0 0 0 0 0 NA NA
## sample_GTATT_Div7 0 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 1 0
## [,406] [,407] [,408] [,409] [,410] [,411] [,412] [,413]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 1 1 0
## sample_CGATGT_Nel4 0 0 1 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 1
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 1
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 1 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 1 0 0 0 1
## sample_GCCAAT_Alt9 0 0 1 0 0 0 0 1
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA 0 0 0 0 0 0 0
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 1
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 1 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA NA NA NA NA NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 NA
## sample_ACAGTG_Cau2 1 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 1 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 1 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 1 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 1 0 0 0 0 0 0 0
## sample_CTAGC_Cau5 1 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 1 0 0 0 0 0 0 0
## sample_GGACCTA_Cau13 1 0 0 0 0 0 0 NA
## sample_TCACC_Cau1 1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 1 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 1 0 0 0 0 0 0 0
## sample_ACTAT_Div14 1 0 0 0 0 0 0 0
## sample_AGCAT_Div11 1 0 0 0 0 0 0 0
## sample_AGCCC_Div9 1 0 0 0 0 0 0 0
## sample_ATCACG_Div1 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 1 0 0 0 0 0 0 0
## sample_CGATGT_Div3 1 0 0 0 0 0 0 0
## sample_CTAGC_Div2 1 0 0 0 0 0 0 0
## sample_CTTGA_Div6 1 0 0 0 1 0 0 0
## sample_CTTGCTT_Div15 1 0 0 0 0 0 0 0
## sample_GTATT_Div10 1 0 0 0 0 0 0 0
## sample_GTATT_Div7 1 0 0 0 0 0 0 0
## sample_TGACCA_Div5 1 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 1 1 0 0 0 0 0 0
## [,414] [,415] [,416] [,417] [,418] [,419] [,420] [,421]
## sample_ACAAA_Nel3 0 1 1 0 0 0 0 0
## sample_ACAGTG_Nel5 0 1 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 1 0 0 1 0 0
## sample_ATGAAAC_Nel10 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 1 1 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 1 0 0 0 0 0
## sample_CTGTA_Nel12 0 1 0 0 0 1 0 0
## sample_CTGTA_Nel9 0 0 1 0 0 0 1 0
## sample_CTTGA_Nel2 0 0 1 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 1 0 0 0 0 0
## sample_GGACCTA_Nel13 0 1 0 0 0 0 0 0
## sample_GTATT_Nel14 0 1 1 0 0 0 0 0
## sample_TCACC_Nel6 0 0 1 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 1 1 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 1 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 1 0 0 0 0 0
## sample_CTGTA_Alt14 0 1 1 0 0 0 0 1
## sample_CTTGA_Alt10 0 0 1 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 1 0 0 0 0 0
## sample_GCCAAT_Alt4 0 1 0 0 0 0 0 1
## sample_GCCAAT_Alt9 0 1 1 0 0 1 0 0
## sample_TTAGGC_Alt2 0 1 1 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 1 1 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 NA 0 0 NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 NA NA NA
## sample_ACTAT_Sub7 0 0 1 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 1 0 0 0 0 0
## sample_AGCCC_Sub11 0 1 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 NA NA 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 1 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 1 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 0 0 0 NA NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 1 0 0 0 NA 0 0 0
## sample_ACAGTG_Cau3 1 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 1 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 1 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 1 0 0 0 0 0 0 NA
## sample_ATGAAAC_Cau12 1 0 0 0 0 NA NA 0
## sample_CTAGC_Cau5 1 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 1 0 0 0 0 0 0 0
## sample_GGACCTA_Cau13 1 0 0 0 1 0 0 0
## sample_TCACC_Cau1 1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 1 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 1 0 0 0 0 0 0 0
## sample_ACTAT_Div14 1 0 0 0 0 0 0 0
## sample_AGCAT_Div11 1 0 0 0 0 0 0 0
## sample_AGCCC_Div9 1 0 0 0 0 0 0 0
## sample_ATCACG_Div1 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 1 0 0 1 0 0 0 0
## sample_CGATGT_Div3 1 0 0 0 0 0 0 0
## sample_CTAGC_Div2 1 0 0 0 0 0 0 0
## sample_CTTGA_Div6 1 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 1 0 0 0 0 NA NA 0
## sample_GTATT_Div10 1 0 0 0 0 0 0 0
## sample_GTATT_Div7 1 0 0 0 0 0 0 0
## sample_TGACCA_Div5 1 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 1 0 0 0 0 0 0 0
## [,422] [,423] [,424] [,425] [,426] [,427] [,428] [,429]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 1 1 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 1 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 1 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 1 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel13 0 0 0 0 1 0 1 0
## sample_GTATT_Nel14 0 0 0 0 0 0 1 0
## sample_TCACC_Nel6 0 0 0 0 0 0 1 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 1 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 1 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 1 0 1 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 1 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 1 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 1 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 1 0
## sample_CTTGA_Alt10 0 1 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 1 0 0 1
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 1 0 1 0
## sample_TTAGGC_Alt8 0 0 0 1 0 1 0 0
## sample_AAAAGTT_Sub15 NA NA NA 0 0 NA NA 1
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 NA 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA NA NA 0 0 0 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 NA 0 0 0 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 NA 0 0 NA 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 1 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 NA 0 0 0 0 0
## sample_AGCCC_Cau7 NA NA 0 0 0 NA 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 NA NA NA 0 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 1 0 0
## sample_TCACC_Cau4 1 0 NA 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 1 0 NA 0 0 1 0 0
## sample_AAAAGTT_Div13 1 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 NA NA NA 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 1 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 NA 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 1 0 0
## sample_CTAGC_Div2 1 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 NA 0 0 0 0 0
## sample_GTATT_Div10 0 0 NA 0 0 0 0 0
## sample_GTATT_Div7 0 0 NA 0 0 0 0 0
## sample_TGACCA_Div5 1 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,430] [,431] [,432] [,433] [,434] [,435] [,436] [,437]
## sample_ACAAA_Nel3 1 1 0 0 1 1 0 1
## sample_ACAGTG_Nel5 0 1 0 0 0 1 0 0
## sample_AGCAT_Nel8 0 1 0 0 0 1 0 0
## sample_ATGAAAC_Nel10 0 1 0 0 0 1 0 0
## sample_ATGAAAC_Nel15 1 1 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 1 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 1 0 0 0 1 0 0
## sample_CTGTA_Nel12 0 1 0 0 0 1 0 0
## sample_CTGTA_Nel9 0 1 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 1 0 0 0 1 0 0
## sample_GGACCTA_Nel11 0 1 0 0 1 0 0 0
## sample_GGACCTA_Nel13 0 1 0 0 0 1 0 0
## sample_GTATT_Nel14 0 1 0 0 0 1 0 0
## sample_TCACC_Nel6 1 1 0 0 0 1 0 0
## sample_TGACCA_Nel1 0 1 0 0 0 1 0 0
## sample_AAAAGTT_Alt12 0 1 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 1 0 0 0 1 0 0
## sample_ACAGTG_Alt3 0 1 0 0 0 1 0 0
## sample_AGCCC_Alt13 0 1 0 0 0 1 0 0
## sample_ATCACG_Alt5 0 1 0 0 1 0 0 0
## sample_ATCACG_Alt7 0 1 0 0 0 1 0 0
## sample_CGATGT_Alt1 0 1 0 0 0 1 0 1
## sample_CTGTA_Alt14 0 1 0 0 0 1 0 1
## sample_CTTGA_Alt10 0 1 0 0 0 0 0 0
## sample_GAATTCA_Alt15 1 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 1 0 0 0 1 0 0
## sample_GCCAAT_Alt9 0 1 0 0 0 1 0 0
## sample_TTAGGC_Alt2 0 1 0 0 0 1 0 0
## sample_TTAGGC_Alt6 0 1 0 0 1 0 0 0
## sample_TTAGGC_Alt8 0 1 0 0 0 1 0 1
## sample_AAAAGTT_Sub15 1 1 NA NA 0 NA NA NA
## sample_ACAAA_Sub1 0 1 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 1 0 0 0 0 0 1
## sample_AGCAT_Sub13 1 1 0 0 0 0 0 1
## sample_AGCCC_Sub11 1 1 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 1 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA 1 0 NA 0 NA NA 0
## sample_GAATTCA_Sub9 1 1 0 0 0 1 0 0
## sample_GGACCTA_Sub10 0 1 0 0 0 0 1 1
## sample_GTATT_Sub12 NA 1 0 NA 0 NA NA 0
## sample_TGACCA_Sub2 0 1 0 0 0 NA NA 0
## sample_ACAGTG_Cau2 0 1 0 NA 0 NA NA 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 1 0
## sample_ACTAT_Cau11 0 1 0 0 0 0 1 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 1 0
## sample_AGCCC_Cau7 0 1 0 0 0 NA NA 0
## sample_ATGAAAC_Cau12 0 1 0 NA 0 0 1 0
## sample_CTAGC_Cau5 0 1 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 1 NA NA 0 NA NA 0
## sample_GGACCTA_Cau13 0 0 NA NA 0 0 1 0
## sample_TCACC_Cau1 0 1 1 1 0 0 1 0
## sample_TCACC_Cau4 0 1 0 0 0 0 1 0
## sample_TGACCA_Cau6 0 1 0 0 0 0 1 0
## sample_AAAAGTT_Div12 0 1 0 0 0 0 1 0
## sample_AAAAGTT_Div13 0 1 0 NA 0 0 1 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 1 0 0 0 NA NA 0
## sample_AGCCC_Div9 0 1 0 1 0 NA NA 0
## sample_ATCACG_Div1 0 1 0 NA 0 0 1 0
## sample_ATGAAAC_Div8 0 1 0 0 0 NA NA 0
## sample_CGATGT_Div3 0 1 0 0 0 NA NA 0
## sample_CTAGC_Div2 0 1 0 0 0 0 1 0
## sample_CTTGA_Div6 0 1 0 0 0 0 1 0
## sample_CTTGCTT_Div15 0 1 0 0 0 NA NA 0
## sample_GTATT_Div10 0 1 0 0 0 0 1 0
## sample_GTATT_Div7 0 1 0 NA 0 0 1 0
## sample_TGACCA_Div5 0 1 0 0 0 0 1 0
## sample_TTAGGC_Div4 0 1 0 1 0 0 1 0
## [,438] [,439] [,440] [,441] [,442] [,443] [,444] [,445]
## sample_ACAAA_Nel3 1 0 0 1 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 1 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 1 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA 0 0 0 0 NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 NA NA 0
## sample_ACTAT_Sub7 1 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 1 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 NA NA 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 NA 0 0 NA
## sample_CTTGCTT_Sub14 0 NA NA 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 1 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA NA 0 0 NA NA 0
## sample_TGACCA_Sub2 0 NA NA 0 0 0 0 0
## sample_ACAGTG_Cau2 0 NA NA 0 1 0 1 NA
## sample_ACAGTG_Cau3 0 1 1 NA 1 0 1 0
## sample_ACTAT_Cau11 0 1 1 0 1 0 1 0
## sample_ACTAT_Cau9 0 NA NA NA 1 0 1 0
## sample_AGCCC_Cau7 0 1 0 0 1 NA NA 0
## sample_ATGAAAC_Cau12 0 NA NA 0 1 NA NA 1
## sample_CTAGC_Cau5 0 1 1 0 1 0 1 0
## sample_CTGTA_Cau8 0 NA NA 0 1 NA NA NA
## sample_GGACCTA_Cau13 0 NA NA 0 1 0 1 NA
## sample_TCACC_Cau1 0 1 0 0 1 0 1 0
## sample_TCACC_Cau4 0 1 1 0 1 NA NA 0
## sample_TGACCA_Cau6 0 1 0 0 0 0 1 0
## sample_AAAAGTT_Div12 0 1 0 0 1 0 1 0
## sample_AAAAGTT_Div13 0 1 1 0 1 0 1 0
## sample_ACTAT_Div14 0 1 0 0 1 0 1 1
## sample_AGCAT_Div11 0 NA NA 0 1 0 1 0
## sample_AGCCC_Div9 0 1 0 0 1 1 1 0
## sample_ATCACG_Div1 0 1 0 0 1 NA NA 0
## sample_ATGAAAC_Div8 0 1 0 0 0 NA NA NA
## sample_CGATGT_Div3 0 1 0 0 1 0 1 0
## sample_CTAGC_Div2 0 1 0 0 1 0 1 0
## sample_CTTGA_Div6 0 1 0 0 0 0 1 0
## sample_CTTGCTT_Div15 0 NA NA 0 NA 0 1 0
## sample_GTATT_Div10 0 NA NA 0 1 0 1 0
## sample_GTATT_Div7 0 1 0 0 1 0 1 0
## sample_TGACCA_Div5 0 1 0 0 1 0 1 1
## sample_TTAGGC_Div4 0 1 0 0 0 0 1 0
## [,446] [,447] [,448] [,449] [,450] [,451] [,452] [,453]
## sample_ACAAA_Nel3 0 0 0 0 NA NA 1 0
## sample_ACAGTG_Nel5 0 1 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 1 0 0 0 0 1 1
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 NA 0 0 1 0
## sample_CGATGT_Nel4 0 1 0 0 0 0 0 NA
## sample_CTAGC_Nel7 0 1 1 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 1 1
## sample_CTGTA_Nel9 0 1 0 0 0 0 1 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel11 0 1 0 0 0 0 1 NA
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 1
## sample_TCACC_Nel6 0 0 0 0 0 0 1 1
## sample_TGACCA_Nel1 0 1 0 0 0 0 1 NA
## sample_AAAAGTT_Alt12 0 1 0 0 0 0 1 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 1 1
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 NA
## sample_AGCCC_Alt13 0 1 0 0 NA NA 1 0
## sample_ATCACG_Alt5 0 1 0 0 0 0 1 0
## sample_ATCACG_Alt7 1 0 0 0 0 0 1 1
## sample_CGATGT_Alt1 0 0 0 NA NA NA 1 0
## sample_CTGTA_Alt14 1 1 0 0 0 0 1 1
## sample_CTTGA_Alt10 1 1 0 NA 0 0 0 1
## sample_GAATTCA_Alt15 0 1 0 NA 0 0 0 0
## sample_GCCAAT_Alt4 0 1 0 0 NA NA 1 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 1 1
## sample_TTAGGC_Alt2 0 1 0 0 NA NA 1 0
## sample_TTAGGC_Alt6 0 1 0 0 0 0 1 NA
## sample_TTAGGC_Alt8 0 0 0 NA 0 0 1 0
## sample_AAAAGTT_Sub15 NA NA NA 0 0 0 NA NA
## sample_ACAAA_Sub1 0 0 0 0 1 1 1 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 1 0
## sample_AGCAT_Sub13 0 1 0 0 0 0 NA 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 1 1
## sample_CGATGT_Sub6 0 0 0 NA 0 0 1 1
## sample_CTTGCTT_Sub14 0 NA 0 0 0 0 1 1
## sample_GAATTCA_Sub9 0 1 0 NA 0 0 1 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 1 1
## sample_GTATT_Sub12 0 0 0 NA NA NA 1 NA
## sample_TGACCA_Sub2 0 0 0 0 NA 0 1 1
## sample_ACAGTG_Cau2 0 0 0 NA NA NA 1 NA
## sample_ACAGTG_Cau3 0 0 0 0 1 0 1 1
## sample_ACTAT_Cau11 0 0 0 0 1 1 1 0
## sample_ACTAT_Cau9 0 0 0 1 1 0 1 1
## sample_AGCCC_Cau7 0 0 0 1 0 0 1 1
## sample_ATGAAAC_Cau12 0 0 0 NA 1 0 1 1
## sample_CTAGC_Cau5 0 0 0 0 1 1 1 NA
## sample_CTGTA_Cau8 0 NA 0 0 NA NA 1 1
## sample_GGACCTA_Cau13 0 NA 0 0 1 0 1 1
## sample_TCACC_Cau1 0 0 0 0 0 0 1 0
## sample_TCACC_Cau4 0 0 0 0 1 0 1 1
## sample_TGACCA_Cau6 0 0 0 0 0 0 1 1
## sample_AAAAGTT_Div12 0 0 0 0 1 0 1 1
## sample_AAAAGTT_Div13 0 0 NA 1 0 0 1 1
## sample_ACTAT_Div14 0 0 0 1 0 0 1 1
## sample_AGCAT_Div11 0 0 NA 0 NA NA 1 NA
## sample_AGCCC_Div9 0 0 0 0 1 0 1 1
## sample_ATCACG_Div1 0 0 0 0 NA NA 1 1
## sample_ATGAAAC_Div8 0 0 0 0 1 1 1 1
## sample_CGATGT_Div3 0 0 0 1 1 0 1 1
## sample_CTAGC_Div2 0 0 0 0 1 0 1 0
## sample_CTTGA_Div6 0 1 0 0 1 0 1 NA
## sample_CTTGCTT_Div15 0 0 NA 0 1 0 1 NA
## sample_GTATT_Div10 0 0 0 0 1 0 1 NA
## sample_GTATT_Div7 NA 0 0 0 NA NA 1 1
## sample_TGACCA_Div5 0 0 0 0 0 0 1 1
## sample_TTAGGC_Div4 0 0 0 1 0 0 1 1
## [,454] [,455] [,456] [,457] [,458] [,459] [,460] [,461]
## sample_ACAAA_Nel3 1 1 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 1 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 1 0 0 0 0 0 1
## sample_ATGAAAC_Nel10 1 1 1 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 1 0 0 0 0 0 1
## sample_CGATGT_Nel4 NA NA 0 0 0 0 0 1
## sample_CTAGC_Nel7 0 1 0 1 0 0 0 1
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 1 0 0 0 0 0 1
## sample_CTTGA_Nel2 0 1 0 0 0 0 0 1
## sample_GGACCTA_Nel11 NA NA 0 0 0 0 0 1
## sample_GGACCTA_Nel13 0 1 1 0 0 0 0 1
## sample_GTATT_Nel14 0 1 0 0 0 0 0 1
## sample_TCACC_Nel6 0 1 0 0 0 0 0 1
## sample_TGACCA_Nel1 NA NA 0 0 0 0 0 1
## sample_AAAAGTT_Alt12 0 1 1 0 0 0 0 0
## sample_ACAAA_Alt11 0 1 0 NA NA NA NA 1
## sample_ACAGTG_Alt3 NA NA 0 NA NA NA NA 1
## sample_AGCCC_Alt13 0 1 1 0 0 0 0 1
## sample_ATCACG_Alt5 0 1 0 0 0 0 0 1
## sample_ATCACG_Alt7 0 0 1 0 0 0 0 1
## sample_CGATGT_Alt1 0 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 1 0 NA NA NA NA 1
## sample_CTTGA_Alt10 0 1 0 0 0 0 0 1
## sample_GAATTCA_Alt15 1 1 0 0 1 0 0 1
## sample_GCCAAT_Alt4 0 1 0 0 0 0 0 1
## sample_GCCAAT_Alt9 0 1 0 NA NA NA NA 1
## sample_TTAGGC_Alt2 0 1 1 0 0 0 0 1
## sample_TTAGGC_Alt6 NA NA 0 NA NA NA NA 1
## sample_TTAGGC_Alt8 0 1 1 0 1 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA NA NA 0
## sample_ACAAA_Sub1 NA NA 1 NA NA NA NA 0
## sample_ACTAT_Sub7 0 1 0 0 0 0 0 0
## sample_AGCAT_Sub13 1 1 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 NA NA NA NA NA 0
## sample_CGATGT_Sub6 0 1 1 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 NA NA NA NA NA 0
## sample_GAATTCA_Sub9 0 1 1 0 0 0 0 1
## sample_GGACCTA_Sub10 0 1 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA 0 0 0 0 0 0
## sample_TGACCA_Sub2 0 0 NA 0 0 0 0 1
## sample_ACAGTG_Cau2 NA NA 0 0 0 0 1 0
## sample_ACAGTG_Cau3 0 0 0 0 0 1 1 0
## sample_ACTAT_Cau11 0 0 0 0 0 1 1 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 1 0
## sample_AGCCC_Cau7 0 0 0 NA NA NA NA 0
## sample_ATGAAAC_Cau12 0 0 0 NA NA NA NA 0
## sample_CTAGC_Cau5 NA NA NA 0 0 1 1 0
## sample_CTGTA_Cau8 0 0 0 NA NA NA NA 0
## sample_GGACCTA_Cau13 0 0 0 NA NA NA NA 0
## sample_TCACC_Cau1 0 0 0 0 0 1 1 0
## sample_TCACC_Cau4 0 0 0 0 0 1 1 0
## sample_TGACCA_Cau6 0 0 0 0 0 1 1 0
## sample_AAAAGTT_Div12 0 0 0 0 0 1 1 0
## sample_AAAAGTT_Div13 0 0 0 0 0 1 1 0
## sample_ACTAT_Div14 0 0 0 0 0 0 1 0
## sample_AGCAT_Div11 NA NA 0 0 0 0 1 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 1 0
## sample_CGATGT_Div3 0 0 0 0 0 1 1 0
## sample_CTAGC_Div2 0 0 0 0 0 0 1 0
## sample_CTTGA_Div6 NA NA 0 0 0 1 1 0
## sample_CTTGCTT_Div15 NA NA 0 0 0 0 0 0
## sample_GTATT_Div10 NA NA 0 0 0 1 1 0
## sample_GTATT_Div7 0 0 0 0 0 0 1 0
## sample_TGACCA_Div5 0 0 0 0 0 1 1 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 1 0
## [,462] [,463] [,464] [,465] [,466] [,467] [,468] [,469]
## sample_ACAAA_Nel3 0 1 0 0 0 1 0 NA
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 1 0 0 0 1 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 1 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 1 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 NA
## sample_CTGTA_Nel12 0 1 0 0 0 1 0 NA
## sample_CTGTA_Nel9 0 1 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 1 0 0 0 0 0 0
## sample_TCACC_Nel6 0 1 0 0 0 0 NA NA
## sample_TGACCA_Nel1 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 1 0 0 0 1 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 NA 0
## sample_ATCACG_Alt5 0 1 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 1 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 1 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 1 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 1 0 0
## sample_GCCAAT_Alt4 0 1 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 NA
## sample_AAAAGTT_Sub15 NA NA NA NA NA NA 0 0
## sample_ACAAA_Sub1 0 1 0 0 0 0 0 NA
## sample_ACTAT_Sub7 0 1 0 0 0 0 0 1
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 NA NA 0 0 0 0 0 NA
## sample_CGATGT_Sub6 0 1 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA NA 0 0 0 0 NA NA
## sample_GAATTCA_Sub9 0 1 0 0 0 1 0 0
## sample_GGACCTA_Sub10 0 1 0 0 0 1 0 0
## sample_GTATT_Sub12 NA NA NA 0 0 NA 0 0
## sample_TGACCA_Sub2 0 1 0 0 0 0 0 NA
## sample_ACAGTG_Cau2 NA NA 1 0 0 0 1 0
## sample_ACAGTG_Cau3 0 0 0 1 0 0 NA 0
## sample_ACTAT_Cau11 1 0 1 0 0 0 0 0
## sample_ACTAT_Cau9 1 0 1 0 0 0 0 0
## sample_AGCCC_Cau7 1 0 NA 0 0 0 0 0
## sample_ATGAAAC_Cau12 1 0 0 0 0 0 1 NA
## sample_CTAGC_Cau5 NA NA 1 0 0 0 1 NA
## sample_CTGTA_Cau8 0 0 0 0 0 0 NA NA
## sample_GGACCTA_Cau13 0 0 1 0 0 0 1 NA
## sample_TCACC_Cau1 1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 NA NA 0 NA NA 0 1 0
## sample_TGACCA_Cau6 1 0 0 1 0 0 0 0
## sample_AAAAGTT_Div12 1 0 0 0 0 0 1 0
## sample_AAAAGTT_Div13 0 0 0 0 1 0 NA 0
## sample_ACTAT_Div14 1 0 0 0 0 0 1 NA
## sample_AGCAT_Div11 NA NA 0 0 0 0 0 0
## sample_AGCCC_Div9 1 0 1 0 0 0 1 0
## sample_ATCACG_Div1 1 0 1 0 0 0 1 NA
## sample_ATGAAAC_Div8 0 0 0 0 0 0 NA NA
## sample_CGATGT_Div3 0 0 1 0 0 0 1 0
## sample_CTAGC_Div2 1 0 0 0 0 0 0 0
## sample_CTTGA_Div6 1 0 0 0 0 0 NA 0
## sample_CTTGCTT_Div15 1 0 NA 0 0 0 NA NA
## sample_GTATT_Div10 1 0 0 0 0 0 1 NA
## sample_GTATT_Div7 1 0 1 0 0 0 NA 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 1 0 0 1 0 0 1 0
## [,470] [,471] [,472] [,473] [,474] [,475] [,476] [,477]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 NA NA 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 1 0 0 1 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 1 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 1 0 0 1 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 1 0 0
## sample_GTATT_Nel14 0 1 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 1 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 1 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 1 0 0 0 1 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 1
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA 0 NA NA NA 0
## sample_ACAAA_Sub1 0 0 0 0 NA 0 NA NA
## sample_ACTAT_Sub7 0 1 0 0 1 0 1 0
## sample_AGCAT_Sub13 0 1 0 0 0 0 1 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 NA 0 0 0 0 NA
## sample_CTTGCTT_Sub14 0 0 NA 0 NA 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 1 0
## sample_GGACCTA_Sub10 0 1 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA NA 0 NA NA 1 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA NA NA 0 0 0 0 1
## sample_ACAGTG_Cau3 1 0 NA 0 0 0 0 1
## sample_ACTAT_Cau11 1 0 1 0 0 0 0 1
## sample_ACTAT_Cau9 1 0 0 0 0 0 0 1
## sample_AGCCC_Cau7 NA NA 1 0 0 0 0 1
## sample_ATGAAAC_Cau12 NA NA NA 0 NA 0 0 1
## sample_CTAGC_Cau5 1 0 1 0 0 0 0 1
## sample_CTGTA_Cau8 1 0 0 NA NA NA 0 1
## sample_GGACCTA_Cau13 NA NA 0 0 0 0 0 1
## sample_TCACC_Cau1 1 0 0 0 0 0 0 1
## sample_TCACC_Cau4 NA NA NA 0 0 0 0 1
## sample_TGACCA_Cau6 1 0 0 0 0 0 0 1
## sample_AAAAGTT_Div12 1 0 0 0 0 0 0 1
## sample_AAAAGTT_Div13 1 0 0 0 0 0 0 1
## sample_ACTAT_Div14 NA NA 0 0 0 0 0 1
## sample_AGCAT_Div11 1 0 0 0 0 0 0 1
## sample_AGCCC_Div9 1 0 0 0 0 0 0 1
## sample_ATCACG_Div1 NA NA 0 0 0 1 0 1
## sample_ATGAAAC_Div8 1 0 0 0 0 0 0 1
## sample_CGATGT_Div3 NA NA 0 0 0 0 0 1
## sample_CTAGC_Div2 NA NA 0 0 0 0 0 1
## sample_CTTGA_Div6 1 0 1 0 0 0 0 1
## sample_CTTGCTT_Div15 NA NA 0 0 0 1 0 1
## sample_GTATT_Div10 1 0 0 0 0 0 0 1
## sample_GTATT_Div7 1 0 1 0 0 NA 0 1
## sample_TGACCA_Div5 1 0 1 1 0 0 0 1
## sample_TTAGGC_Div4 NA NA 1 0 0 0 0 1
## [,478] [,479] [,480] [,481] [,482] [,483] [,484] [,485]
## sample_ACAAA_Nel3 0 1 1 0 0 0 0 1
## sample_ACAGTG_Nel5 0 0 1 0 1 0 0 1
## sample_AGCAT_Nel8 0 0 1 0 0 0 0 1
## sample_ATGAAAC_Nel10 0 1 1 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 1 0 0 1 0 0 1
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 1
## sample_CTAGC_Nel7 0 0 1 1 0 0 0 1
## sample_CTGTA_Nel12 0 0 0 0 1 0 0 1
## sample_CTGTA_Nel9 0 1 0 0 1 0 0 1
## sample_CTTGA_Nel2 0 1 1 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 1 0 0 0 0 1
## sample_GGACCTA_Nel13 0 1 1 0 0 0 0 1
## sample_GTATT_Nel14 0 1 1 0 0 0 0 1
## sample_TCACC_Nel6 0 0 0 0 1 0 0 1
## sample_TGACCA_Nel1 0 0 1 1 0 0 0 1
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0 1
## sample_ACAAA_Alt11 0 0 1 1 0 0 0 1
## sample_ACAGTG_Alt3 0 0 0 0 1 0 0 1
## sample_AGCCC_Alt13 0 0 1 1 0 0 0 1
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 1
## sample_ATCACG_Alt7 0 1 1 0 0 0 0 1
## sample_CGATGT_Alt1 0 0 1 0 1 0 0 1
## sample_CTGTA_Alt14 0 0 0 0 1 0 0 1
## sample_CTTGA_Alt10 0 0 0 0 1 0 0 1
## sample_GAATTCA_Alt15 0 1 0 0 0 0 0 1
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 1
## sample_GCCAAT_Alt9 0 1 0 0 1 0 0 0
## sample_TTAGGC_Alt2 0 1 1 0 0 0 0 1
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 1
## sample_TTAGGC_Alt8 0 0 1 0 1 0 0 1
## sample_AAAAGTT_Sub15 0 NA NA NA NA NA NA NA
## sample_ACAAA_Sub1 NA 1 NA NA NA NA NA NA
## sample_ACTAT_Sub7 0 1 1 0 0 0 0 1
## sample_AGCAT_Sub13 0 0 1 0 1 0 0 1
## sample_AGCCC_Sub11 0 1 NA NA NA NA NA NA
## sample_CGATGT_Sub6 NA 1 NA NA NA NA NA NA
## sample_CTTGCTT_Sub14 0 1 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 1 1 0 0 0 0 1
## sample_GGACCTA_Sub10 0 1 1 0 0 0 0 1
## sample_GTATT_Sub12 NA 0 0 0 0 0 0 1
## sample_TGACCA_Sub2 0 1 0 0 0 0 0 0
## sample_ACAGTG_Cau2 1 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 1 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 1 0 0 0 0 1 1 0
## sample_ACTAT_Cau9 1 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 1 0 NA NA NA NA NA NA
## sample_ATGAAAC_Cau12 1 0 NA NA NA NA 1 0
## sample_CTAGC_Cau5 1 0 1 0 0 1 0 0
## sample_CTGTA_Cau8 1 NA NA NA NA NA NA NA
## sample_GGACCTA_Cau13 1 0 0 0 0 0 1 0
## sample_TCACC_Cau1 1 0 0 0 0 0 0 1
## sample_TCACC_Cau4 1 0 0 0 0 1 0 0
## sample_TGACCA_Cau6 1 0 1 0 0 0 0 0
## sample_AAAAGTT_Div12 1 0 0 0 0 0 1 0
## sample_AAAAGTT_Div13 1 0 1 0 0 0 0 0
## sample_ACTAT_Div14 1 0 0 0 0 0 1 0
## sample_AGCAT_Div11 1 0 0 0 0 0 1 0
## sample_AGCCC_Div9 1 0 0 0 0 0 0 0
## sample_ATCACG_Div1 1 0 1 0 0 1 1 0
## sample_ATGAAAC_Div8 1 0 0 0 0 0 0 0
## sample_CGATGT_Div3 1 0 0 0 0 0 1 0
## sample_CTAGC_Div2 1 0 0 0 0 0 0 0
## sample_CTTGA_Div6 1 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 1 0 NA NA NA NA NA NA
## sample_GTATT_Div10 1 0 1 0 0 0 0 0
## sample_GTATT_Div7 1 NA 0 0 0 0 0 0
## sample_TGACCA_Div5 1 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 1 0 1 0 0 0 0 0
## [,486] [,487] [,488] [,489] [,490] [,491] [,492] [,493]
## sample_ACAAA_Nel3 1 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 1 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 1 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 1 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 1 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 1 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 1 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 1 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 1 0 0 0 0 0 0 0
## sample_GTATT_Nel14 1 0 0 0 0 0 0 0
## sample_TCACC_Nel6 1 1 0 0 0 0 0 0
## sample_TGACCA_Nel1 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 1 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 1 0 0 0 1 0 0 0
## sample_ACAGTG_Alt3 1 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 1 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 1 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 1 0 0 0 1 0 0 0
## sample_CGATGT_Alt1 1 0 0 0 0 0 0 1
## sample_CTGTA_Alt14 1 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 1 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 1 0 0 0 0 0 1 0
## sample_GCCAAT_Alt4 1 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 1 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 1 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 0 NA NA NA 0
## sample_ACAAA_Sub1 NA 0 0 0 NA NA 0 0
## sample_ACTAT_Sub7 1 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 1 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 NA 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 NA 0 0 0 NA NA 0 0
## sample_CTTGCTT_Sub14 0 0 0 NA 0 0 0 0
## sample_GAATTCA_Sub9 1 0 0 0 1 0 0 0
## sample_GGACCTA_Sub10 1 0 0 0 0 0 0 0
## sample_GTATT_Sub12 1 0 0 0 NA NA 0 NA
## sample_TGACCA_Sub2 0 0 0 NA 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 1 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 1 0 1 0 0
## sample_ACTAT_Cau11 0 0 0 1 0 1 0 0
## sample_ACTAT_Cau9 0 0 0 1 0 1 0 0
## sample_AGCCC_Cau7 NA 0 0 1 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 1 NA NA 0 0
## sample_CTAGC_Cau5 0 0 0 1 0 1 0 0
## sample_CTGTA_Cau8 NA 0 0 1 NA NA 0 0
## sample_GGACCTA_Cau13 0 0 0 1 0 1 0 0
## sample_TCACC_Cau1 1 0 0 1 0 1 0 0
## sample_TCACC_Cau4 0 0 0 1 0 1 0 0
## sample_TGACCA_Cau6 0 0 1 1 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 1 0 1 0 0
## sample_AAAAGTT_Div13 0 0 0 1 0 1 0 0
## sample_ACTAT_Div14 0 0 0 1 0 1 0 0
## sample_AGCAT_Div11 0 0 0 1 0 1 0 0
## sample_AGCCC_Div9 0 0 0 1 0 1 0 0
## sample_ATCACG_Div1 0 0 0 1 0 1 0 0
## sample_ATGAAAC_Div8 0 0 0 1 0 1 0 0
## sample_CGATGT_Div3 0 0 0 1 0 1 0 0
## sample_CTAGC_Div2 0 0 0 1 NA NA 0 0
## sample_CTTGA_Div6 0 0 1 1 0 0 0 0
## sample_CTTGCTT_Div15 NA 0 1 1 0 1 0 0
## sample_GTATT_Div10 0 0 0 1 0 1 0 0
## sample_GTATT_Div7 0 0 0 1 0 1 0 0
## sample_TGACCA_Div5 0 0 0 1 0 1 0 0
## sample_TTAGGC_Div4 0 0 1 1 0 1 0 0
## [,494] [,495] [,496] [,497] [,498] [,499] [,500] [,501]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 NA NA 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 NA NA 0 0 0 0 0 0
## sample_GGACCTA_Nel11 1 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 NA NA 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 0 0 0 0 0
## sample_ACAAA_Sub1 0 0 0 0 0 0 1 1
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 1 0 0 0 0
## sample_CGATGT_Sub6 NA NA 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA NA 0 0 NA 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA 0 0 NA 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA NA 0 1 NA 1 0 0
## sample_ACAGTG_Cau3 0 0 0 1 NA 1 0 0
## sample_ACTAT_Cau11 0 0 0 1 0 1 0 0
## sample_ACTAT_Cau9 0 0 0 1 1 1 0 0
## sample_AGCCC_Cau7 0 0 0 1 0 1 0 0
## sample_ATGAAAC_Cau12 NA NA 0 1 NA 1 0 0
## sample_CTAGC_Cau5 NA NA 0 1 1 1 0 0
## sample_CTGTA_Cau8 0 0 0 1 0 1 0 0
## sample_GGACCTA_Cau13 0 0 0 1 1 1 0 0
## sample_TCACC_Cau1 0 1 0 0 0 1 0 0
## sample_TCACC_Cau4 NA NA 0 1 1 1 0 0
## sample_TGACCA_Cau6 0 0 0 1 1 1 0 0
## sample_AAAAGTT_Div12 NA NA 0 1 1 1 0 0
## sample_AAAAGTT_Div13 NA NA 0 1 1 1 0 0
## sample_ACTAT_Div14 0 0 0 1 NA 1 0 0
## sample_AGCAT_Div11 NA NA 0 1 NA 1 0 0
## sample_AGCCC_Div9 0 0 0 1 0 1 0 0
## sample_ATCACG_Div1 0 0 0 1 NA 1 0 0
## sample_ATGAAAC_Div8 0 0 0 1 NA 1 0 0
## sample_CGATGT_Div3 0 0 0 1 1 1 0 0
## sample_CTAGC_Div2 0 0 0 1 0 1 0 0
## sample_CTTGA_Div6 NA NA 0 1 0 1 0 0
## sample_CTTGCTT_Div15 0 0 0 1 NA 1 0 0
## sample_GTATT_Div10 NA NA 0 1 NA 1 0 0
## sample_GTATT_Div7 NA NA 0 1 1 1 0 0
## sample_TGACCA_Div5 0 1 0 0 1 1 0 0
## sample_TTAGGC_Div4 0 1 0 1 1 1 0 0
## [,502] [,503] [,504] [,505] [,506] [,507] [,508] [,509]
## sample_ACAAA_Nel3 0 0 0 1 0 NA 0 0
## sample_ACAGTG_Nel5 0 0 0 1 0 1 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 1 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 1 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 1 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 NA 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 NA 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 1 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 1 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 NA 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 1 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 1 0 0
## sample_GTATT_Nel14 0 0 0 0 0 1 0 1
## sample_TCACC_Nel6 0 0 0 0 0 1 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 1 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 1 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 1 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 NA 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 NA NA 0
## sample_ATCACG_Alt7 0 0 0 0 0 1 0 0
## sample_CGATGT_Alt1 0 0 0 1 0 1 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 1 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 1 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 1 0 0
## sample_GCCAAT_Alt4 0 0 0 1 0 1 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Sub15 0 0 0 NA NA 1 NA NA
## sample_ACAAA_Sub1 1 1 1 0 NA 1 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 NA 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 1 0 0
## sample_AGCCC_Sub11 0 0 0 0 NA 1 NA 0
## sample_CGATGT_Sub6 0 0 0 NA 0 1 0 0
## sample_CTTGCTT_Sub14 0 0 0 NA NA 1 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 1 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 1 0 0
## sample_GTATT_Sub12 0 0 0 NA 0 1 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 1 1 0
## sample_ACAGTG_Cau2 0 0 0 0 1 0 NA 0
## sample_ACAGTG_Cau3 0 0 0 0 1 0 0 NA
## sample_ACTAT_Cau11 0 0 0 0 1 NA 0 0
## sample_ACTAT_Cau9 0 0 0 0 1 NA 0 0
## sample_AGCCC_Cau7 0 0 0 0 1 1 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 1 1 0 NA
## sample_CTAGC_Cau5 0 0 0 0 1 0 0 0
## sample_CTGTA_Cau8 0 0 0 0 1 0 0 NA
## sample_GGACCTA_Cau13 0 0 0 0 1 0 0 NA
## sample_TCACC_Cau1 0 0 0 0 1 1 0 0
## sample_TCACC_Cau4 0 0 0 0 1 1 NA 0
## sample_TGACCA_Cau6 0 0 0 0 1 NA 0 0
## sample_AAAAGTT_Div12 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 1 0 0 0
## sample_ACTAT_Div14 0 0 0 0 1 0 0 NA
## sample_AGCAT_Div11 0 0 0 0 1 0 0 NA
## sample_AGCCC_Div9 0 0 0 0 1 NA 0 0
## sample_ATCACG_Div1 0 0 0 0 1 NA 0 0
## sample_ATGAAAC_Div8 0 0 0 0 1 0 0 0
## sample_CGATGT_Div3 0 0 0 0 1 0 0 0
## sample_CTAGC_Div2 0 0 0 0 1 1 0 0
## sample_CTTGA_Div6 0 0 0 0 1 NA 0 0
## sample_CTTGCTT_Div15 0 0 0 0 1 0 0 NA
## sample_GTATT_Div10 0 0 0 0 1 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0 NA
## sample_TGACCA_Div5 0 0 0 0 1 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 1 0 0 0
## [,510] [,511] [,512] [,513] [,514] [,515] [,516] [,517]
## sample_ACAAA_Nel3 1 0 1 0 0 0 0 0
## sample_ACAGTG_Nel5 0 1 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 1 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 1 1 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 1 0 0 0 0 0 0
## sample_CGATGT_Nel4 1 1 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 1 1 0 0 0 0 0
## sample_CTGTA_Nel12 1 1 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 1 1 0 0 0 0 0
## sample_CTTGA_Nel2 0 1 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 1 1 0 0 0 0 0
## sample_GGACCTA_Nel13 1 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 1 0 0 0 0 0 0
## sample_TCACC_Nel6 0 1 1 0 0 0 0 0
## sample_TGACCA_Nel1 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 1 1 0 0 0 0 0
## sample_ACAAA_Alt11 0 1 1 0 0 0 0 0
## sample_ACAGTG_Alt3 0 1 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 1 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 1 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 1 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 1 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 1 0 0 0 0 0 1
## sample_GCCAAT_Alt4 0 1 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 1 1 0 0 0 0 0
## sample_TTAGGC_Alt8 0 1 0 1 1 1 1 0
## sample_AAAAGTT_Sub15 NA NA 0 0 0 0 0 0
## sample_ACAAA_Sub1 0 NA 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 1 0 0 0 0 0 0
## sample_AGCCC_Sub11 1 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 NA 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA NA 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 1 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA 0 0 0 0 0 0
## sample_TGACCA_Sub2 NA 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA 0 1 0 0 0 0 0
## sample_ACAGTG_Cau3 0 NA 1 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 1 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 1 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Cau12 NA NA 1 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 1 0 0 0 0 0
## sample_CTGTA_Cau8 0 NA 1 0 0 0 0 0
## sample_GGACCTA_Cau13 0 0 1 0 0 0 0 0
## sample_TCACC_Cau1 0 0 1 0 0 0 0 0
## sample_TCACC_Cau4 0 0 1 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 1 0 0 0 0 0
## sample_ACTAT_Div14 0 0 1 0 0 0 0 0
## sample_AGCAT_Div11 NA 0 1 0 0 0 0 0
## sample_AGCCC_Div9 0 0 1 0 0 0 0 0
## sample_ATCACG_Div1 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 1 0 0 0 0 0
## sample_CGATGT_Div3 0 0 1 0 0 0 0 0
## sample_CTAGC_Div2 0 0 1 0 0 0 0 0
## sample_CTTGA_Div6 0 0 1 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 1 0 0 0 0 0
## sample_GTATT_Div10 0 0 1 0 0 0 0 0
## sample_GTATT_Div7 0 NA 1 0 0 0 0 0
## sample_TGACCA_Div5 0 0 1 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 1 0 0 0 0 0
## [,518] [,519] [,520] [,521] [,522] [,523] [,524] [,525]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 1 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 1
## sample_GTATT_Nel14 0 0 0 0 0 0 0 NA
## sample_TCACC_Nel6 0 0 0 0 0 0 0 1
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 1
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 1
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 1
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 NA NA NA NA NA
## sample_ACAAA_Sub1 0 0 0 NA NA 0 NA 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 1
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 1
## sample_AGCCC_Sub11 0 NA 1 1 1 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 NA NA
## sample_CTTGCTT_Sub14 0 0 0 1 1 NA 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 1
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 NA
## sample_GTATT_Sub12 0 0 0 1 1 0 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 1
## sample_ACAGTG_Cau2 0 1 1 NA NA 0 0 NA
## sample_ACAGTG_Cau3 0 0 1 0 0 1 0 1
## sample_ACTAT_Cau11 0 1 1 0 0 0 0 1
## sample_ACTAT_Cau9 0 1 1 0 0 0 0 1
## sample_AGCCC_Cau7 0 0 1 0 0 0 0 1
## sample_ATGAAAC_Cau12 0 1 0 0 0 NA NA 1
## sample_CTAGC_Cau5 0 1 1 0 0 0 0 1
## sample_CTGTA_Cau8 0 NA 1 0 0 0 0 NA
## sample_GGACCTA_Cau13 0 1 1 0 0 0 0 NA
## sample_TCACC_Cau1 0 1 1 0 0 0 0 1
## sample_TCACC_Cau4 0 1 1 0 0 0 0 NA
## sample_TGACCA_Cau6 0 1 1 0 0 0 0 1
## sample_AAAAGTT_Div12 0 NA 1 0 0 0 0 1
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 1
## sample_ACTAT_Div14 0 0 1 0 0 0 0 1
## sample_AGCAT_Div11 0 NA 1 0 0 0 1 NA
## sample_AGCCC_Div9 0 0 1 0 0 0 0 1
## sample_ATCACG_Div1 0 0 0 0 0 0 0 1
## sample_ATGAAAC_Div8 0 1 1 0 0 0 0 NA
## sample_CGATGT_Div3 0 0 1 0 0 0 0 1
## sample_CTAGC_Div2 0 1 1 0 0 0 1 1
## sample_CTTGA_Div6 0 1 0 0 0 0 0 1
## sample_CTTGCTT_Div15 0 1 1 0 0 0 0 NA
## sample_GTATT_Div10 0 1 1 0 0 0 0 NA
## sample_GTATT_Div7 0 1 1 0 0 0 0 NA
## sample_TGACCA_Div5 0 1 0 0 0 0 0 1
## sample_TTAGGC_Div4 0 0 1 0 0 0 1 1
## [,526] [,527] [,528] [,529] [,530] [,531] [,532] [,533]
## sample_ACAAA_Nel3 0 0 1 0 0 0 0 1
## sample_ACAGTG_Nel5 0 1 1 1 0 0 0 0
## sample_AGCAT_Nel8 0 1 1 1 0 0 0 1
## sample_ATGAAAC_Nel10 0 0 1 0 0 0 0 1
## sample_ATGAAAC_Nel15 0 1 0 1 0 0 0 1
## sample_CGATGT_Nel4 0 1 0 1 0 0 0 1
## sample_CTAGC_Nel7 0 1 1 0 0 0 0 1
## sample_CTGTA_Nel12 0 1 1 1 0 0 0 0
## sample_CTGTA_Nel9 0 1 1 1 0 0 0 1
## sample_CTTGA_Nel2 0 0 1 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 1 0 0 0 0 1
## sample_GGACCTA_Nel13 0 1 1 0 0 0 0 1
## sample_GTATT_Nel14 0 1 0 1 0 0 0 1
## sample_TCACC_Nel6 0 1 0 1 0 0 1 1
## sample_TGACCA_Nel1 0 1 1 1 0 0 0 1
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0 0
## sample_ACAAA_Alt11 0 1 0 1 0 1 0 0
## sample_ACAGTG_Alt3 0 0 1 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 1 0 1 0 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 1 0 0 0 0 0
## sample_CGATGT_Alt1 0 1 1 0 0 0 0 0
## sample_CTGTA_Alt14 0 1 0 1 1 0 0 1
## sample_CTTGA_Alt10 0 1 1 1 0 0 0 1
## sample_GAATTCA_Alt15 0 1 1 0 1 0 0 1
## sample_GCCAAT_Alt4 0 1 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 1 1 0 1 0 0 1
## sample_TTAGGC_Alt2 0 1 1 0 0 0 0 1
## sample_TTAGGC_Alt6 0 1 0 1 0 0 0 0
## sample_TTAGGC_Alt8 0 1 1 1 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA 1 0 NA NA
## sample_ACAAA_Sub1 0 NA NA NA 1 0 0 1
## sample_ACTAT_Sub7 0 1 0 1 0 0 0 1
## sample_AGCAT_Sub13 0 0 1 0 1 0 0 1
## sample_AGCCC_Sub11 NA 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 NA NA 0 NA
## sample_CTTGCTT_Sub14 0 NA NA NA NA NA NA 1
## sample_GAATTCA_Sub9 0 1 0 1 0 0 0 1
## sample_GGACCTA_Sub10 1 1 0 1 1 0 0 1
## sample_GTATT_Sub12 NA 0 0 0 NA NA 0 NA
## sample_TGACCA_Sub2 NA 0 0 0 1 0 0 1
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 NA NA NA 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 NA NA NA 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 NA 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 NA NA NA 0 0 NA 0
## sample_GTATT_Div10 0 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,534] [,535] [,536] [,537] [,538] [,539] [,540] [,541]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 1
## sample_AGCAT_Nel8 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 NA 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 1
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 1
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 1
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 1
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA 0 NA NA
## sample_ACAAA_Sub1 NA NA NA 0 0 0 NA NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 NA NA
## sample_CGATGT_Sub6 NA NA 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA 0 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA 0 0 0 0 NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 1 0 0 0 0 NA NA
## sample_ACAGTG_Cau3 0 1 0 1 1 0 1 0
## sample_ACTAT_Cau11 0 1 1 1 1 0 1 0
## sample_ACTAT_Cau9 0 1 1 1 1 0 1 0
## sample_AGCCC_Cau7 0 NA 0 1 1 0 NA NA
## sample_ATGAAAC_Cau12 0 1 1 1 1 NA 1 0
## sample_CTAGC_Cau5 0 1 0 1 1 0 1 0
## sample_CTGTA_Cau8 0 NA 0 NA NA 0 NA NA
## sample_GGACCTA_Cau13 0 NA 0 NA NA 0 1 0
## sample_TCACC_Cau1 0 1 1 1 1 0 1 0
## sample_TCACC_Cau4 0 1 0 0 0 0 1 0
## sample_TGACCA_Cau6 0 1 1 1 1 0 1 0
## sample_AAAAGTT_Div12 0 1 0 0 0 0 1 0
## sample_AAAAGTT_Div13 0 0 0 NA NA 0 1 0
## sample_ACTAT_Div14 0 1 0 1 1 0 1 0
## sample_AGCAT_Div11 0 0 1 0 0 0 1 0
## sample_AGCCC_Div9 0 1 0 1 1 0 1 0
## sample_ATCACG_Div1 0 1 0 1 1 0 1 0
## sample_ATGAAAC_Div8 NA 0 0 1 1 0 1 0
## sample_CGATGT_Div3 0 0 0 1 1 1 1 0
## sample_CTAGC_Div2 0 1 0 1 1 0 1 0
## sample_CTTGA_Div6 0 1 1 0 0 0 1 0
## sample_CTTGCTT_Div15 NA 1 0 1 1 0 1 0
## sample_GTATT_Div10 0 1 NA 0 0 0 1 0
## sample_GTATT_Div7 NA 0 0 1 1 0 1 0
## sample_TGACCA_Div5 0 0 1 1 1 0 1 0
## sample_TTAGGC_Div4 0 0 0 1 1 0 1 0
## [,542] [,543] [,544] [,545] [,546] [,547] [,548] [,549]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA NA 0 0
## sample_ACAAA_Sub1 1 0 0 0 0 NA 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 1 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 NA 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 NA 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 NA 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 1 1 0 0
## sample_ACAGTG_Cau2 0 0 1 NA 0 0 0 0
## sample_ACAGTG_Cau3 0 NA NA 1 0 0 0 0
## sample_ACTAT_Cau11 0 1 1 1 0 0 0 0
## sample_ACTAT_Cau9 0 0 1 NA 0 0 0 0
## sample_AGCCC_Cau7 0 0 1 1 0 0 0 0
## sample_ATGAAAC_Cau12 0 NA NA NA 0 0 0 0
## sample_CTAGC_Cau5 0 0 1 1 0 0 0 0
## sample_CTGTA_Cau8 0 NA NA 1 0 0 0 0
## sample_GGACCTA_Cau13 0 0 1 NA 0 0 0 0
## sample_TCACC_Cau1 0 0 1 1 0 0 0 0
## sample_TCACC_Cau4 0 0 1 1 0 NA 0 0
## sample_TGACCA_Cau6 0 1 1 1 0 0 0 0
## sample_AAAAGTT_Div12 0 0 1 NA 0 0 0 0
## sample_AAAAGTT_Div13 0 1 1 NA 0 0 0 0
## sample_ACTAT_Div14 0 0 1 NA 0 0 0 0
## sample_AGCAT_Div11 0 0 1 1 0 0 1 0
## sample_AGCCC_Div9 0 0 1 1 0 0 0 0
## sample_ATCACG_Div1 0 1 1 1 0 0 0 0
## sample_ATGAAAC_Div8 0 0 1 NA 0 0 0 0
## sample_CGATGT_Div3 0 0 1 0 0 0 0 0
## sample_CTAGC_Div2 0 0 1 1 0 0 0 0
## sample_CTTGA_Div6 0 0 1 NA 0 0 0 0
## sample_CTTGCTT_Div15 0 NA NA NA 0 0 0 0
## sample_GTATT_Div10 0 1 1 1 0 0 0 0
## sample_GTATT_Div7 0 1 1 NA 0 0 0 0
## sample_TGACCA_Div5 0 1 1 1 0 0 0 0
## sample_TTAGGC_Div4 0 1 1 0 0 0 0 0
## [,550] [,551] [,552] [,553] [,554] [,555] [,556] [,557]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 1 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 1 0 1 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 1 0 0
## sample_CTGTA_Nel12 1 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel11 0 0 0 0 0 1 0 1
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 1
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 1
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 1 0 1
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 1
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 0 0 NA 0 NA
## sample_ACAAA_Sub1 NA 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 NA 0 1 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA NA 0 0 0 0 NA NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA 0 0 0 0 NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 0 NA 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 1 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 NA 0 0 0 NA 0 0 0
## sample_CTAGC_Cau5 0 1 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 NA 0 0 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 1 0 0 1 0 0 0
## sample_TCACC_Cau4 0 0 0 0 NA 0 0 0
## sample_TGACCA_Cau6 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 1 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 NA 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 1 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 0 0
## sample_GTATT_Div10 0 1 0 0 0 0 0 0
## sample_GTATT_Div7 0 NA 0 0 0 0 0 0
## sample_TGACCA_Div5 0 1 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 1 0 0 0
## [,558] [,559] [,560] [,561] [,562] [,563] [,564] [,565]
## sample_ACAAA_Nel3 1 1 0 0 0 0 0 0
## sample_ACAGTG_Nel5 1 1 0 0 0 0 0 0
## sample_AGCAT_Nel8 1 1 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 1 NA 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 NA 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 1 0 0 0 0 0 0
## sample_CTAGC_Nel7 1 1 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 1 0 0 1 1 0 1
## sample_CTGTA_Nel9 0 1 0 0 0 1 0 1
## sample_CTTGA_Nel2 1 NA 0 0 1 1 0 1
## sample_GGACCTA_Nel11 0 1 1 0 0 0 0 0
## sample_GGACCTA_Nel13 0 NA 0 0 0 0 0 0
## sample_GTATT_Nel14 1 0 0 0 1 1 0 1
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 1 1 1 0 0 0 0 0
## sample_ACAAA_Alt11 0 1 0 0 1 1 0 1
## sample_ACAGTG_Alt3 1 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 1 1 0 0 0 0 0
## sample_ATCACG_Alt5 1 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 1 1 1 0 0 0 0 0
## sample_CGATGT_Alt1 0 1 0 0 1 1 0 1
## sample_CTGTA_Alt14 1 1 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 1 1 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 1 1 0 1
## sample_GCCAAT_Alt4 0 1 0 0 1 1 0 1
## sample_GCCAAT_Alt9 1 1 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt6 1 1 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 1 1 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 0 NA NA NA NA
## sample_ACAAA_Sub1 1 1 0 0 1 1 0 1
## sample_ACTAT_Sub7 1 1 0 0 0 0 0 0
## sample_AGCAT_Sub13 1 1 0 0 1 1 1 1
## sample_AGCCC_Sub11 1 NA 0 0 0 0 0 0
## sample_CGATGT_Sub6 1 0 NA NA 0 0 0 0
## sample_CTTGCTT_Sub14 NA NA 0 0 NA NA NA NA
## sample_GAATTCA_Sub9 1 1 0 0 0 0 0 0
## sample_GGACCTA_Sub10 1 0 1 0 1 1 1 1
## sample_GTATT_Sub12 0 0 0 0 NA NA NA NA
## sample_TGACCA_Sub2 1 0 0 0 NA NA NA NA
## sample_ACAGTG_Cau2 0 0 0 1 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 1 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 1 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 1 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 1 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 1 0 0 0 0
## sample_CTGTA_Cau8 0 0 NA NA 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 1 0 0 0 0
## sample_TCACC_Cau1 0 0 0 1 0 0 0 0
## sample_TCACC_Cau4 0 0 0 1 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 1 0 0 0 0
## sample_ACTAT_Div14 0 0 0 1 0 0 0 0
## sample_AGCAT_Div11 0 0 0 1 0 0 0 0
## sample_AGCCC_Div9 0 0 0 1 0 0 0 0
## sample_ATCACG_Div1 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 1 0 0 0 0
## sample_CGATGT_Div3 0 0 0 1 0 0 0 0
## sample_CTAGC_Div2 0 0 0 1 0 0 0 0
## sample_CTTGA_Div6 0 0 0 1 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 1 0 0 0 0
## sample_GTATT_Div10 0 0 0 1 0 0 0 0
## sample_GTATT_Div7 0 0 0 1 0 0 0 0
## sample_TGACCA_Div5 0 0 0 1 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 1 0 0 0 0
## [,566] [,567] [,568] [,569] [,570] [,571] [,572] [,573]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 1 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 1 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 1 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 1 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 1 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 NA NA
## sample_ATCACG_Alt7 0 0 0 0 0 0 1 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 1 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 1 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 1 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Sub15 NA 0 NA NA NA 0 NA NA
## sample_ACAAA_Sub1 0 0 0 0 NA 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 1 0
## sample_AGCAT_Sub13 1 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 1 0
## sample_CGATGT_Sub6 0 0 0 0 NA 0 0 0
## sample_CTTGCTT_Sub14 NA 0 NA NA NA NA NA NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 1 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 NA NA NA NA NA NA
## sample_TGACCA_Sub2 NA 0 NA NA 1 0 0 0
## sample_ACAGTG_Cau2 0 0 NA NA 1 0 NA NA
## sample_ACAGTG_Cau3 0 0 NA NA 1 0 0 1
## sample_ACTAT_Cau11 0 0 1 1 1 0 0 0
## sample_ACTAT_Cau9 0 0 0 1 1 0 0 0
## sample_AGCCC_Cau7 0 0 NA NA NA 0 0 NA
## sample_ATGAAAC_Cau12 0 1 0 1 NA 0 NA NA
## sample_CTAGC_Cau5 0 0 0 1 1 0 0 0
## sample_CTGTA_Cau8 0 0 NA NA NA 0 NA NA
## sample_GGACCTA_Cau13 0 0 0 1 1 0 0 1
## sample_TCACC_Cau1 0 1 0 1 1 0 0 0
## sample_TCACC_Cau4 0 0 NA NA 1 0 0 1
## sample_TGACCA_Cau6 0 0 0 1 1 0 0 1
## sample_AAAAGTT_Div12 0 0 NA NA 1 0 0 1
## sample_AAAAGTT_Div13 0 0 NA NA 1 0 1 0
## sample_ACTAT_Div14 0 0 0 1 1 1 0 1
## sample_AGCAT_Div11 0 0 NA NA 1 0 NA NA
## sample_AGCCC_Div9 0 0 0 1 1 0 0 1
## sample_ATCACG_Div1 0 0 0 1 1 0 0 1
## sample_ATGAAAC_Div8 0 0 0 1 1 0 0 0
## sample_CGATGT_Div3 0 0 0 1 1 0 0 1
## sample_CTAGC_Div2 0 0 NA NA 1 0 0 1
## sample_CTTGA_Div6 0 0 0 1 1 0 0 0
## sample_CTTGCTT_Div15 0 1 0 1 NA 0 NA NA
## sample_GTATT_Div10 0 0 NA NA 1 1 0 1
## sample_GTATT_Div7 0 0 NA NA 1 0 0 1
## sample_TGACCA_Div5 0 0 0 1 1 0 0 0
## sample_TTAGGC_Div4 0 0 NA NA 1 0 0 0
## [,574] [,575] [,576] [,577] [,578] [,579] [,580] [,581]
## sample_ACAAA_Nel3 1 0 0 0 0 0 1 0
## sample_ACAGTG_Nel5 0 0 0 0 1 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Nel10 0 0 0 0 1 0 1 0
## sample_ATGAAAC_Nel15 0 0 0 0 1 0 1 1
## sample_CGATGT_Nel4 0 0 0 0 1 0 0 0
## sample_CTAGC_Nel7 0 0 1 0 1 1 1 0
## sample_CTGTA_Nel12 0 0 0 1 1 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 1 0 1 0
## sample_CTTGA_Nel2 0 0 0 0 1 0 1 0
## sample_GGACCTA_Nel11 0 0 0 0 0 1 1 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 1 0
## sample_GTATT_Nel14 0 0 0 0 0 0 1 0
## sample_TCACC_Nel6 0 0 0 0 1 0 1 0
## sample_TGACCA_Nel1 1 0 0 1 1 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 1 0
## sample_ACAAA_Alt11 0 0 0 0 0 1 0 0
## sample_ACAGTG_Alt3 0 0 0 0 1 0 1 0
## sample_AGCCC_Alt13 0 0 0 0 1 0 1 0
## sample_ATCACG_Alt5 0 0 0 0 0 1 1 0
## sample_ATCACG_Alt7 0 0 0 0 1 0 1 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 1 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 1 0 1 0
## sample_GAATTCA_Alt15 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 1 0
## sample_GCCAAT_Alt9 0 0 0 0 1 0 1 0
## sample_TTAGGC_Alt2 0 0 0 NA 1 0 1 0
## sample_TTAGGC_Alt6 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 1 0 1 0
## sample_AAAAGTT_Sub15 NA NA 0 NA NA NA NA NA
## sample_ACAAA_Sub1 NA 0 1 1 NA NA NA NA
## sample_ACTAT_Sub7 0 0 0 NA 0 0 1 0
## sample_AGCAT_Sub13 0 0 0 0 1 0 1 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 1 0
## sample_CGATGT_Sub6 NA 0 0 0 NA NA NA NA
## sample_CTTGCTT_Sub14 0 NA 0 0 NA NA 1 0
## sample_GAATTCA_Sub9 0 0 0 0 1 0 1 0
## sample_GGACCTA_Sub10 0 0 1 0 1 0 1 0
## sample_GTATT_Sub12 NA NA 0 0 1 0 NA NA
## sample_TGACCA_Sub2 NA NA 0 0 0 0 1 0
## sample_ACAGTG_Cau2 0 NA 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 NA 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 NA 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 NA NA 0 NA NA 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 0 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 NA 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 NA 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 0 0
## sample_GTATT_Div10 0 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 1 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,582] [,583] [,584] [,585] [,586] [,587] [,588] [,589]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Nel10 0 1 0 1 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 1 0 0 0 0
## sample_CGATGT_Nel4 0 1 0 1 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 1 1 0 0 0
## sample_CTGTA_Nel9 0 0 0 1 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 1 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 1 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 1 0 0 0 0
## sample_TCACC_Nel6 0 0 0 1 0 0 0 0
## sample_TGACCA_Nel1 0 1 0 1 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 1 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 1 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 1 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 1 0 0 1 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 1 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 NA 1 NA 0 0 0
## sample_ACAAA_Sub1 0 0 0 0 NA 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 1 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 1 NA 0 0 0 0
## sample_CGATGT_Sub6 0 0 NA NA 0 0 0 1
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 NA NA
## sample_GAATTCA_Sub9 0 1 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 1 0 1 0 0 0 0
## sample_GTATT_Sub12 0 0 0 1 0 0 NA NA
## sample_TGACCA_Sub2 0 0 0 1 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 0 NA 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 1 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 NA 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 0 NA
## sample_CTAGC_Cau5 0 0 0 0 0 1 0 0
## sample_CTGTA_Cau8 0 0 0 0 0 NA 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 NA 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 NA
## sample_TGACCA_Cau6 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 NA 0
## sample_AAAAGTT_Div13 0 0 0 0 0 1 NA 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 NA 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 NA 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 NA NA 0
## sample_GTATT_Div10 0 0 0 0 0 NA 0 0
## sample_GTATT_Div7 0 0 0 0 0 NA 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 1 0
## [,590] [,591] [,592] [,593] [,594] [,595] [,596] [,597]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 1 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 NA 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 1
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 NA 0 0 1 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 1
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 NA 0 0 0 NA
## sample_ACAAA_Sub1 NA NA 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 NA 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA NA 0 0 0 0 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA 0 0 0 0 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0 NA
## sample_ACAGTG_Cau3 0 0 0 0 0 0 1 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 NA 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 NA 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 NA NA 0 NA 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 NA 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 NA 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 1 0 1 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 1 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 1 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 NA 0 0 NA 0 0 0 NA
## sample_GTATT_Div10 0 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 1 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,598] [,599] [,600] [,601] [,602] [,603] [,604] [,605]
## sample_ACAAA_Nel3 0 0 0 0 0 0 1 0
## sample_ACAGTG_Nel5 0 0 1 0 1 0 1 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Nel15 0 1 0 0 0 0 1 0
## sample_CGATGT_Nel4 0 1 0 0 0 0 NA NA
## sample_CTAGC_Nel7 0 0 0 0 0 0 1 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 1 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 NA NA
## sample_GGACCTA_Nel13 0 0 0 0 0 0 1 0
## sample_GTATT_Nel14 0 0 0 0 0 0 1 0
## sample_TCACC_Nel6 0 0 0 0 0 0 1 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 1 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 1 0 0 0 NA NA
## sample_AGCCC_Alt13 0 0 1 0 0 0 1 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 1 0
## sample_ATCACG_Alt7 0 0 1 0 0 0 1 0
## sample_CGATGT_Alt1 0 0 1 0 0 0 1 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 1 0
## sample_GAATTCA_Alt15 0 0 1 0 0 0 NA NA
## sample_GCCAAT_Alt4 0 0 1 0 0 0 1 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 1 0
## sample_TTAGGC_Alt2 0 0 1 0 0 0 1 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 1 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Sub15 0 0 0 0 NA 0 1 0
## sample_ACAAA_Sub1 0 NA NA 0 NA 0 1 0
## sample_ACTAT_Sub7 0 0 1 0 0 0 1 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 1 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 NA NA
## sample_CGATGT_Sub6 0 0 1 0 0 0 1 0
## sample_CTTGCTT_Sub14 0 0 0 0 NA 0 NA NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 1 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 1 0
## sample_GTATT_Sub12 NA 0 0 0 NA 0 1 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 NA NA
## sample_ACAGTG_Cau2 NA 0 0 0 0 0 NA NA
## sample_ACAGTG_Cau3 1 0 0 0 0 0 0 1
## sample_ACTAT_Cau11 1 0 0 0 0 0 0 1
## sample_ACTAT_Cau9 1 0 0 0 0 0 0 1
## sample_AGCCC_Cau7 1 0 0 0 0 0 0 1
## sample_ATGAAAC_Cau12 1 0 0 0 0 0 0 1
## sample_CTAGC_Cau5 1 0 0 0 0 0 0 1
## sample_CTGTA_Cau8 1 0 0 0 NA 1 0 1
## sample_GGACCTA_Cau13 1 0 0 0 0 0 0 1
## sample_TCACC_Cau1 1 0 0 0 0 0 0 1
## sample_TCACC_Cau4 1 0 0 1 0 0 0 1
## sample_TGACCA_Cau6 1 0 0 0 0 0 0 1
## sample_AAAAGTT_Div12 1 0 0 0 0 0 0 1
## sample_AAAAGTT_Div13 1 0 0 0 0 0 0 1
## sample_ACTAT_Div14 1 0 0 0 0 0 0 1
## sample_AGCAT_Div11 NA 0 0 0 0 0 0 1
## sample_AGCCC_Div9 1 0 0 0 0 0 0 1
## sample_ATCACG_Div1 1 0 0 0 0 0 0 1
## sample_ATGAAAC_Div8 1 0 0 0 0 0 0 1
## sample_CGATGT_Div3 1 0 0 0 0 0 0 0
## sample_CTAGC_Div2 1 0 0 0 0 0 0 1
## sample_CTTGA_Div6 1 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 NA 0 0 0 0 0 0 1
## sample_GTATT_Div10 NA 0 0 0 0 1 0 1
## sample_GTATT_Div7 1 0 0 0 0 0 0 1
## sample_TGACCA_Div5 1 0 0 0 0 0 0 1
## sample_TTAGGC_Div4 1 0 0 0 0 0 0 1
## [,606] [,607] [,608] [,609] [,610] [,611] [,612] [,613]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 1 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 1 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 1 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 1 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 1 0
## sample_TGACCA_Nel1 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 1 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 1 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 1 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 1 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 1 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 1 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA 0 0 0 0 NA NA NA
## sample_ACAAA_Sub1 NA 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 1 NA NA NA NA 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA 0 0 0 0 NA NA NA
## sample_GAATTCA_Sub9 1 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA NA NA NA NA NA NA
## sample_TGACCA_Sub2 1 0 0 0 0 NA NA NA
## sample_ACAGTG_Cau2 0 0 1 1 1 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 NA 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 NA NA NA
## sample_ATGAAAC_Cau12 0 0 0 0 0 NA NA NA
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 NA NA NA NA NA NA NA NA
## sample_GGACCTA_Cau13 0 NA NA NA NA NA NA NA
## sample_TCACC_Cau1 0 0 1 1 1 0 0 0
## sample_TCACC_Cau4 0 NA NA NA NA 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 1 1 1 0 0 0
## sample_AAAAGTT_Div13 0 0 1 1 1 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 NA NA NA NA 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 NA NA NA
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 1 1 1 0 0 0
## sample_CTAGC_Div2 0 0 1 1 1 1 0 0
## sample_CTTGA_Div6 0 NA NA NA NA 0 0 0
## sample_CTTGCTT_Div15 NA 0 0 0 0 NA NA NA
## sample_GTATT_Div10 NA 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0 1
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,614] [,615] [,616] [,617] [,618] [,619] [,620] [,621]
## sample_ACAAA_Nel3 0 0 1 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 0 1 0 0 1 0 0
## sample_CGATGT_Nel4 0 0 1 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 1 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 1 0 0 1 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 1 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 1 0 0 1 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 1 0 0 1 0 0
## sample_AGCCC_Alt13 0 0 1 1 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 1 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 1 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 1 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 1 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt2 0 0 0 1 0 1 0 0
## sample_TTAGGC_Alt6 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA 0 NA 0 0
## sample_ACAAA_Sub1 0 0 1 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 1 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 1 0 0 1 0 0
## sample_AGCCC_Sub11 0 0 1 0 0 1 0 0
## sample_CGATGT_Sub6 NA NA NA NA 0 0 0 0
## sample_CTTGCTT_Sub14 NA NA NA NA 0 NA 0 0
## sample_GAATTCA_Sub9 0 0 1 0 0 1 0 0
## sample_GGACCTA_Sub10 0 0 1 0 0 1 0 0
## sample_GTATT_Sub12 0 0 1 0 NA NA 0 0
## sample_TGACCA_Sub2 NA NA NA NA 0 0 0 0
## sample_ACAGTG_Cau2 0 1 0 0 0 NA 0 0
## sample_ACAGTG_Cau3 0 1 0 0 0 0 1 0
## sample_ACTAT_Cau11 0 1 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 1 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 1 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 1 0 0 0 NA 0 NA
## sample_CTAGC_Cau5 0 1 0 0 0 0 0 0
## sample_CTGTA_Cau8 NA NA NA NA 0 0 0 0
## sample_GGACCTA_Cau13 0 1 0 0 0 NA 0 0
## sample_TCACC_Cau1 0 1 0 0 0 0 0 0
## sample_TCACC_Cau4 0 1 0 0 0 0 0 NA
## sample_TGACCA_Cau6 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 1 0 0 0 0 1 1
## sample_ACTAT_Div14 0 1 0 0 0 0 0 0
## sample_AGCAT_Div11 0 1 0 0 0 NA 0 0
## sample_AGCCC_Div9 0 1 0 0 0 0 0 0
## sample_ATCACG_Div1 0 1 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 1 0 0 0 0 0 0
## sample_CGATGT_Div3 0 1 0 0 0 0 0 0
## sample_CTAGC_Div2 0 1 0 0 0 0 0 0
## sample_CTTGA_Div6 0 1 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 1 0 0 0 0 0 0
## sample_GTATT_Div10 0 1 0 0 0 0 0 0
## sample_GTATT_Div7 0 1 0 0 0 0 0 0
## sample_TGACCA_Div5 0 1 0 0 0 0 0 1
## sample_TTAGGC_Div4 0 1 0 0 0 0 0 0
## [,622] [,623] [,624] [,625] [,626] [,627] [,628] [,629]
## sample_ACAAA_Nel3 0 1 1 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 1 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 1 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 1 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 1 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 1 0 0 0 0
## sample_ACAAA_Alt11 0 1 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 1 1 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 1 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 0 NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 NA NA 0
## sample_ACTAT_Sub7 0 0 1 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 1 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 NA 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 NA
## sample_CTTGCTT_Sub14 NA 0 0 0 0 NA NA 0
## sample_GAATTCA_Sub9 0 0 1 0 0 1 0 0
## sample_GGACCTA_Sub10 0 0 1 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 1 0 0 NA NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0 1
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 1
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 1
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 NA
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 0 1
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 1
## sample_CTGTA_Cau8 0 0 0 0 0 0 0 NA
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 NA
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 NA
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 1
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 1
## sample_AGCAT_Div11 0 0 0 0 0 0 0 1
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 1 1
## sample_CTTGA_Div6 0 0 0 0 0 0 0 1
## sample_CTTGCTT_Div15 0 0 0 0 0 0 0 NA
## sample_GTATT_Div10 0 0 0 0 0 0 0 1
## sample_GTATT_Div7 0 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 1
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 1
## [,630] [,631] [,632] [,633] [,634] [,635] [,636] [,637]
## sample_ACAAA_Nel3 0 1 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 1 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 1 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 1 0 1 0 0 0 0
## sample_CTAGC_Nel7 0 1 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 1 1
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 1 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 1 0 0 0 0 0 0
## sample_GTATT_Nel14 0 1 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 1 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 1 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 1 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 1 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 1 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 1 0 0 0 1 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA NA NA NA
## sample_ACAAA_Sub1 0 0 0 NA NA 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 NA NA NA NA 0
## sample_CGATGT_Sub6 0 0 0 NA NA NA NA 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 NA NA 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA NA 0 0 NA NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 NA NA NA NA 0 0 0
## sample_ACAGTG_Cau3 0 0 1 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 NA NA 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 NA NA 0 1 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 1 NA NA 0
## sample_TCACC_Cau1 0 0 0 0 1 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 NA NA 0 0 0
## sample_AGCCC_Div9 0 0 0 0 1 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 1 0 0 0
## sample_CTTGA_Div6 0 0 0 0 1 0 0 0
## sample_CTTGCTT_Div15 0 NA NA NA NA 0 0 0
## sample_GTATT_Div10 0 0 0 0 1 0 0 0
## sample_GTATT_Div7 0 NA NA 0 1 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,638] [,639] [,640] [,641] [,642] [,643] [,644] [,645]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 1 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 1 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 NA NA NA NA NA 0
## sample_TCACC_Nel6 0 0 NA NA NA NA NA 0
## sample_TGACCA_Nel1 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA 1 1 0 0 1 0
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 NA NA NA NA NA 0
## sample_CGATGT_Sub6 0 NA NA NA NA NA NA 0
## sample_CTTGCTT_Sub14 0 NA NA NA NA NA NA 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 NA NA NA NA NA 0
## sample_TGACCA_Sub2 0 0 NA NA NA NA NA 0
## sample_ACAGTG_Cau2 NA 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 NA NA NA NA NA 0
## sample_ACTAT_Cau9 0 0 0 0 0 1 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 NA 0 0 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 1 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 NA NA NA NA NA 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 NA NA NA NA NA 0
## sample_ATGAAAC_Div8 NA 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 1 0 1
## sample_CTAGC_Div2 0 0 0 0 0 1 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 NA 0 0 0 0 0 0
## sample_GTATT_Div10 0 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 1 0 0
## [,646] [,647] [,648] [,649] [,650] [,651] [,652] [,653]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 1 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 NA NA NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA NA NA NA NA NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 NA
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0 NA
## sample_ACAGTG_Cau3 1 0 1 1 1 0 0 1
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 1
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 1
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 1
## sample_ATGAAAC_Cau12 NA NA NA NA NA 0 0 NA
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 1
## sample_CTGTA_Cau8 0 0 0 0 0 0 0 1
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 1
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 NA NA NA NA NA 0 0 1
## sample_AAAAGTT_Div12 NA NA NA NA NA 0 0 1
## sample_AAAAGTT_Div13 NA NA NA NA NA 0 0 1
## sample_ACTAT_Div14 0 0 0 0 0 0 0 1
## sample_AGCAT_Div11 0 0 0 0 0 0 0 NA
## sample_AGCCC_Div9 NA NA NA NA NA 0 0 1
## sample_ATCACG_Div1 0 0 0 0 0 0 0 1
## sample_ATGAAAC_Div8 NA NA NA NA NA 0 0 1
## sample_CGATGT_Div3 0 0 0 0 0 0 0 1
## sample_CTAGC_Div2 0 0 0 0 0 0 0 1
## sample_CTTGA_Div6 NA NA NA NA NA 0 0 1
## sample_CTTGCTT_Div15 0 0 0 0 0 NA NA 1
## sample_GTATT_Div10 NA NA NA NA NA 0 0 1
## sample_GTATT_Div7 0 0 0 0 0 NA NA 1
## sample_TGACCA_Div5 0 0 0 0 0 0 0 1
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 1
## [,654] [,655] [,656] [,657] [,658] [,659] [,660] [,661]
## sample_ACAAA_Nel3 0 0 0 0 0 1 0 1
## sample_ACAGTG_Nel5 1 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 NA
## sample_CGATGT_Nel4 1 0 0 0 0 0 0 1
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 1
## sample_CTGTA_Nel12 0 0 0 NA 0 0 0 0
## sample_CTGTA_Nel9 0 0 1 NA 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 NA 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 1 0 0 1 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 1 0 0 NA 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 NA 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 1 0 0 0 0 0 0 1
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 NA 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 NA 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 NA 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 NA 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA 0 NA 0 NA NA 0 0
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 NA 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 NA 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA 0 0 0 0 NA 0 0
## sample_GAATTCA_Sub9 0 0 0 NA 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 NA 0 0
## sample_TGACCA_Sub2 NA 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA NA 0 0 NA 0 0 0
## sample_ACAGTG_Cau3 0 1 0 NA 1 0 0 0
## sample_ACTAT_Cau11 0 0 0 NA 1 0 0 0
## sample_ACTAT_Cau9 0 1 0 0 1 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 1 NA 0 0
## sample_ATGAAAC_Cau12 NA 0 0 0 1 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 1 0 0 NA
## sample_CTGTA_Cau8 0 0 0 0 1 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 1 0 0 0
## sample_TCACC_Cau1 0 1 0 0 1 0 0 0
## sample_TCACC_Cau4 0 NA 0 0 1 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Div13 0 1 0 0 1 0 0 0
## sample_ACTAT_Div14 0 1 0 0 1 0 0 0
## sample_AGCAT_Div11 NA 0 0 0 1 0 0 0
## sample_AGCCC_Div9 0 1 0 0 1 0 0 0
## sample_ATCACG_Div1 0 1 0 0 1 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 1 0 0 0
## sample_CGATGT_Div3 0 1 0 0 1 0 0 0
## sample_CTAGC_Div2 0 0 0 0 1 0 0 0
## sample_CTTGA_Div6 0 0 0 0 1 0 0 0
## sample_CTTGCTT_Div15 0 NA 0 0 NA 0 0 0
## sample_GTATT_Div10 0 0 0 0 1 0 0 0
## sample_GTATT_Div7 0 1 0 0 NA 0 0 0
## sample_TGACCA_Div5 0 0 0 NA 1 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 1 0 0 0
## [,662] [,663] [,664] [,665] [,666] [,667] [,668] [,669]
## sample_ACAAA_Nel3 1 0 0 1 NA NA NA 0
## sample_ACAGTG_Nel5 1 0 0 1 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 1 NA NA NA 0
## sample_ATGAAAC_Nel10 1 0 0 1 0 0 0 0
## sample_ATGAAAC_Nel15 1 0 0 1 0 0 0 0
## sample_CGATGT_Nel4 1 0 1 1 0 0 0 0
## sample_CTAGC_Nel7 1 0 0 1 0 0 0 0
## sample_CTGTA_Nel12 1 0 0 1 0 0 0 0
## sample_CTGTA_Nel9 1 0 0 1 0 0 0 0
## sample_CTTGA_Nel2 1 0 0 1 NA NA NA 0
## sample_GGACCTA_Nel11 0 0 0 1 NA NA NA 0
## sample_GGACCTA_Nel13 1 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 1 0 0 0 0
## sample_TCACC_Nel6 1 0 0 1 0 0 0 0
## sample_TGACCA_Nel1 1 0 0 1 0 0 0 0
## sample_AAAAGTT_Alt12 1 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 1 0 0 1 0 0 0 0
## sample_ACAGTG_Alt3 1 0 0 1 0 0 0 0
## sample_AGCCC_Alt13 1 0 0 1 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 1 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 1 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 1 0 0 0 0
## sample_CTGTA_Alt14 1 0 0 1 0 0 0 0
## sample_CTTGA_Alt10 1 0 0 1 0 0 0 0
## sample_GAATTCA_Alt15 1 0 0 1 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 1 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt2 1 0 0 1 0 0 0 0
## sample_TTAGGC_Alt6 1 0 0 1 0 0 0 0
## sample_TTAGGC_Alt8 1 0 0 1 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA 0 0 0 0
## sample_ACAAA_Sub1 1 NA 0 1 NA NA NA 0
## sample_ACTAT_Sub7 0 0 0 1 NA NA NA 0
## sample_AGCAT_Sub13 1 0 0 1 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 NA 0 0 0 0
## sample_CGATGT_Sub6 1 NA NA NA 0 0 0 NA
## sample_CTTGCTT_Sub14 0 0 1 NA 0 0 0 0
## sample_GAATTCA_Sub9 1 0 0 1 0 0 0 0
## sample_GGACCTA_Sub10 0 0 1 1 NA NA NA 0
## sample_GTATT_Sub12 0 NA 0 1 0 0 0 0
## sample_TGACCA_Sub2 1 0 1 1 0 0 0 0
## sample_ACAGTG_Cau2 0 NA 0 0 0 0 0 1
## sample_ACAGTG_Cau3 0 NA 0 0 0 0 0 1
## sample_ACTAT_Cau11 0 0 0 1 NA NA NA 1
## sample_ACTAT_Cau9 0 0 0 0 NA NA NA 1
## sample_AGCCC_Cau7 0 NA 0 NA 0 0 0 1
## sample_ATGAAAC_Cau12 0 NA 0 0 0 0 0 1
## sample_CTAGC_Cau5 0 0 0 0 1 1 1 1
## sample_CTGTA_Cau8 0 NA 0 NA NA NA NA NA
## sample_GGACCTA_Cau13 0 1 0 NA 0 0 0 1
## sample_TCACC_Cau1 0 0 0 1 0 0 0 1
## sample_TCACC_Cau4 0 1 0 0 0 0 0 1
## sample_TGACCA_Cau6 0 0 0 0 NA NA NA 1
## sample_AAAAGTT_Div12 0 0 0 0 NA NA NA 1
## sample_AAAAGTT_Div13 0 0 0 0 NA NA NA 1
## sample_ACTAT_Div14 0 1 0 0 NA NA NA 1
## sample_AGCAT_Div11 0 0 0 0 0 0 0 1
## sample_AGCCC_Div9 0 0 0 0 0 0 0 1
## sample_ATCACG_Div1 0 NA 0 0 NA NA NA 1
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 1
## sample_CGATGT_Div3 0 0 0 0 0 0 0 1
## sample_CTAGC_Div2 0 NA 0 0 0 0 0 1
## sample_CTTGA_Div6 0 1 0 0 0 0 0 1
## sample_CTTGCTT_Div15 0 NA 0 0 NA NA NA 1
## sample_GTATT_Div10 0 0 0 0 0 0 0 1
## sample_GTATT_Div7 0 0 0 0 0 0 0 1
## sample_TGACCA_Div5 0 0 0 0 NA NA NA 1
## sample_TTAGGC_Div4 0 1 0 0 NA NA NA 1
## [,670] [,671] [,672] [,673] [,674] [,675] [,676] [,677]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 1 0 0 0 0 0 1
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 1 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 1 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 1 0 0 0 1
## sample_TGACCA_Nel1 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 1 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 1
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 1 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 NA 0 1 NA NA
## sample_ACAAA_Sub1 0 0 0 NA 0 NA 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 1 0 1
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 NA NA 0 0 0 0 1
## sample_CGATGT_Sub6 NA 0 0 0 0 1 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 NA NA NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 1
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA NA NA NA NA NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 1 0
## sample_ACAGTG_Cau2 1 0 1 0 1 0 1 0
## sample_ACAGTG_Cau3 1 0 0 0 1 0 1 0
## sample_ACTAT_Cau11 1 0 0 0 1 0 1 0
## sample_ACTAT_Cau9 1 0 0 0 1 0 1 0
## sample_AGCCC_Cau7 1 0 1 0 1 0 1 0
## sample_ATGAAAC_Cau12 1 0 0 0 1 0 1 0
## sample_CTAGC_Cau5 1 0 1 0 1 0 1 0
## sample_CTGTA_Cau8 NA 0 0 0 1 0 1 0
## sample_GGACCTA_Cau13 1 0 1 0 1 0 1 0
## sample_TCACC_Cau1 1 0 0 0 1 0 1 0
## sample_TCACC_Cau4 1 0 1 0 1 0 1 0
## sample_TGACCA_Cau6 0 0 0 0 1 0 1 0
## sample_AAAAGTT_Div12 1 0 1 0 1 0 1 0
## sample_AAAAGTT_Div13 1 0 1 0 1 0 1 0
## sample_ACTAT_Div14 1 0 0 0 1 0 1 0
## sample_AGCAT_Div11 1 0 1 0 1 0 1 0
## sample_AGCCC_Div9 0 0 1 0 1 0 0 0
## sample_ATCACG_Div1 1 0 0 0 1 0 1 0
## sample_ATGAAAC_Div8 0 0 1 0 1 0 1 0
## sample_CGATGT_Div3 1 0 0 0 1 0 1 0
## sample_CTAGC_Div2 1 0 0 0 1 0 1 0
## sample_CTTGA_Div6 1 0 1 0 1 0 1 0
## sample_CTTGCTT_Div15 1 0 1 0 1 0 1 0
## sample_GTATT_Div10 1 0 0 0 1 0 1 0
## sample_GTATT_Div7 1 0 0 0 1 0 1 0
## sample_TGACCA_Div5 1 0 0 0 1 0 1 0
## sample_TTAGGC_Div4 1 0 0 0 1 0 1 0
## [,678] [,679] [,680] [,681] [,682] [,683] [,684] [,685]
## sample_ACAAA_Nel3 0 0 0 0 1 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 1 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 1 0 0 0
## sample_CGATGT_Nel4 0 0 0 NA NA NA NA 0
## sample_CTAGC_Nel7 0 0 0 0 1 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 1 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 1 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 1 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 1 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 1 0 0 0
## sample_GTATT_Nel14 0 0 0 NA NA NA NA 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 0 NA NA NA NA 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 1 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 1 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 1 0 0 0
## sample_CGATGT_Alt1 0 0 0 NA NA NA NA 1
## sample_CTGTA_Alt14 0 0 0 0 1 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 1 0 0 0
## sample_GAATTCA_Alt15 0 0 0 NA NA NA NA 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 NA
## sample_GCCAAT_Alt9 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 1 0 0 1
## sample_TTAGGC_Alt6 0 0 0 NA NA NA NA 0
## sample_TTAGGC_Alt8 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA 0 1 0 0 NA
## sample_ACAAA_Sub1 0 1 1 NA NA NA NA 1
## sample_ACTAT_Sub7 0 0 0 0 1 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 1 0 0 0
## sample_AGCCC_Sub11 0 0 1 0 0 0 0 0
## sample_CGATGT_Sub6 NA NA NA NA NA NA NA 0
## sample_CTTGCTT_Sub14 0 0 0 NA NA NA NA 0
## sample_GAATTCA_Sub9 0 0 0 0 1 0 0 1
## sample_GGACCTA_Sub10 0 0 0 0 1 0 0 0
## sample_GTATT_Sub12 0 0 0 0 1 0 0 1
## sample_TGACCA_Sub2 0 0 0 NA NA NA NA 0
## sample_ACAGTG_Cau2 NA NA NA NA NA NA NA 0
## sample_ACAGTG_Cau3 0 0 1 1 1 1 1 0
## sample_ACTAT_Cau11 1 0 1 1 1 1 1 0
## sample_ACTAT_Cau9 0 1 1 1 1 1 1 0
## sample_AGCCC_Cau7 1 0 1 0 0 0 0 NA
## sample_ATGAAAC_Cau12 NA NA NA NA NA NA NA 1
## sample_CTAGC_Cau5 1 0 1 1 1 1 1 0
## sample_CTGTA_Cau8 NA NA NA 0 0 0 0 NA
## sample_GGACCTA_Cau13 NA NA NA NA NA NA NA NA
## sample_TCACC_Cau1 0 1 1 NA NA NA NA 0
## sample_TCACC_Cau4 1 0 1 NA NA NA NA NA
## sample_TGACCA_Cau6 0 1 1 0 0 0 0 0
## sample_AAAAGTT_Div12 0 1 1 NA NA NA NA 0
## sample_AAAAGTT_Div13 1 0 1 0 0 0 0 0
## sample_ACTAT_Div14 1 0 1 0 0 0 0 0
## sample_AGCAT_Div11 NA NA NA NA NA NA NA 0
## sample_AGCCC_Div9 1 0 1 NA NA NA NA NA
## sample_ATCACG_Div1 NA NA NA 1 1 1 1 1
## sample_ATGAAAC_Div8 NA NA NA 1 1 1 1 NA
## sample_CGATGT_Div3 1 1 1 1 0 0 0 0
## sample_CTAGC_Div2 1 0 1 NA NA NA NA 1
## sample_CTTGA_Div6 0 1 1 0 0 0 0 0
## sample_CTTGCTT_Div15 NA NA NA 1 1 1 1 1
## sample_GTATT_Div10 1 0 1 NA NA NA NA 0
## sample_GTATT_Div7 0 1 1 0 0 0 0 1
## sample_TGACCA_Div5 0 1 1 0 0 0 0 1
## sample_TTAGGC_Div4 0 1 1 0 0 0 0 0
## [,686] [,687] [,688] [,689] [,690] [,691] [,692] [,693]
## sample_ACAAA_Nel3 0 0 0 0 1 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 1 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 1 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 1 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 1 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 1 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 1 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 1 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 NA NA NA NA
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 1 1 0 0 0
## sample_AGCCC_Alt13 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 1 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 1 0 0 0
## sample_CTGTA_Alt14 0 0 0 1 1 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 1 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 NA 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Sub15 NA 0 0 0 NA NA NA NA
## sample_ACAAA_Sub1 0 NA NA NA NA NA NA NA
## sample_ACTAT_Sub7 0 0 0 0 1 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 NA NA NA NA NA NA NA
## sample_GAATTCA_Sub9 0 0 0 0 1 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA NA NA NA NA NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 NA NA NA NA
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 NA 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 0 0
## sample_CTAGC_Cau5 1 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 NA 0 0 0 0 0 0 0
## sample_GGACCTA_Cau13 NA 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 NA 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 NA NA NA NA
## sample_AAAAGTT_Div13 1 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 NA NA NA NA
## sample_AGCCC_Div9 0 1 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 1 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 1 1 1
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 NA NA NA NA
## sample_GTATT_Div10 0 0 0 0 NA NA NA NA
## sample_GTATT_Div7 1 0 0 0 NA NA NA NA
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 1 1 1
## [,694] [,695] [,696] [,697] [,698] [,699] [,700] [,701]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 1
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 NA NA 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 1 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 1 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 1 0 0 1
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 1
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 1
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 0 0 NA NA NA
## sample_ACAAA_Sub1 NA NA 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA NA 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA 0 0 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA NA NA NA NA 0 0 0
## sample_ACAGTG_Cau3 0 0 0 1 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 1 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 1 0 0 0 0
## sample_GGACCTA_Cau13 0 0 1 1 0 0 0 0
## sample_TCACC_Cau1 0 0 0 1 0 0 0 0
## sample_TCACC_Cau4 0 0 NA NA NA 0 0 0
## sample_TGACCA_Cau6 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Div12 NA NA 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 NA NA NA NA NA 0 0 0
## sample_AGCCC_Div9 0 0 0 1 0 0 0 0
## sample_ATCACG_Div1 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 1 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 NA NA 0 0 0 0 0 0
## sample_GTATT_Div10 NA NA 0 1 0 0 0 0
## sample_GTATT_Div7 NA NA 0 1 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 1 1 0 1 0 0 0 0
## [,702] [,703] [,704] [,705] [,706] [,707] [,708] [,709]
## sample_ACAAA_Nel3 0 1 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 1 1 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 1 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel15 0 1 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 1 0 0 0
## sample_CTGTA_Nel12 1 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 1 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 1 0 0 1 0 0 0
## sample_GGACCTA_Nel11 0 1 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 1 0 0 0 0 0 0
## sample_GTATT_Nel14 0 1 0 0 0 0 0 0
## sample_TCACC_Nel6 0 1 0 0 1 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Alt12 0 1 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 1 0 0 0 1 0 0 0
## sample_ATCACG_Alt5 0 1 0 0 1 0 0 0
## sample_ATCACG_Alt7 1 1 0 0 1 0 1 0
## sample_CGATGT_Alt1 1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 1 0 0 1 0 0 0
## sample_CTTGA_Alt10 1 1 0 0 1 0 0 0
## sample_GAATTCA_Alt15 0 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 1 1
## sample_GCCAAT_Alt9 0 1 0 0 1 0 0 1
## sample_TTAGGC_Alt2 0 1 0 0 1 0 0 0
## sample_TTAGGC_Alt6 1 1 0 0 0 0 1 0
## sample_TTAGGC_Alt8 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Sub15 0 NA 0 0 0 0 NA NA
## sample_ACAAA_Sub1 NA 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 1 0 0 1 0 0 0
## sample_AGCAT_Sub13 0 1 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 NA 0 0 0 0 0 NA
## sample_CGATGT_Sub6 0 1 0 0 NA NA 0 0
## sample_CTTGCTT_Sub14 NA NA 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 1 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 1 0 0 0
## sample_GTATT_Sub12 0 NA NA NA NA NA 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 1 NA 0 1 0 0
## sample_ACAGTG_Cau3 0 0 1 NA 0 1 0 0
## sample_ACTAT_Cau11 0 0 1 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 1 1 0 1 0 0
## sample_AGCCC_Cau7 0 0 1 NA 0 1 0 0
## sample_ATGAAAC_Cau12 0 0 1 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 1 NA 0 1 0 0
## sample_CTGTA_Cau8 NA 0 1 NA NA NA 0 0
## sample_GGACCTA_Cau13 0 0 1 0 0 1 0 0
## sample_TCACC_Cau1 0 0 1 0 0 1 0 0
## sample_TCACC_Cau4 0 NA 1 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 1 0 0 1 0 0
## sample_AAAAGTT_Div12 0 0 1 1 0 1 0 0
## sample_AAAAGTT_Div13 0 0 1 1 0 1 0 0
## sample_ACTAT_Div14 0 0 1 0 0 0 0 0
## sample_AGCAT_Div11 0 0 NA 0 0 0 0 0
## sample_AGCCC_Div9 0 0 1 0 0 1 0 0
## sample_ATCACG_Div1 0 0 1 0 0 1 0 0
## sample_ATGAAAC_Div8 0 0 1 0 0 1 0 0
## sample_CGATGT_Div3 0 0 1 1 0 1 0 0
## sample_CTAGC_Div2 0 0 1 0 0 1 0 0
## sample_CTTGA_Div6 0 0 1 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 1 0 0 0 0 0
## sample_GTATT_Div10 0 0 1 NA 0 1 0 0
## sample_GTATT_Div7 0 0 1 1 0 0 0 0
## sample_TGACCA_Div5 0 0 1 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 1 0 0 1 0 0
## [,710] [,711] [,712] [,713] [,714] [,715] [,716] [,717]
## sample_ACAAA_Nel3 1 0 0 1 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 1 0 1 0
## sample_AGCAT_Nel8 1 0 0 1 0 0 0 1
## sample_ATGAAAC_Nel10 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 1 0 0 0
## sample_CGATGT_Nel4 1 0 NA NA NA NA NA NA
## sample_CTAGC_Nel7 1 0 NA NA NA NA NA NA
## sample_CTGTA_Nel12 0 0 0 1 0 0 0 0
## sample_CTGTA_Nel9 1 0 0 0 1 0 0 0
## sample_CTTGA_Nel2 0 0 0 1 0 0 0 1
## sample_GGACCTA_Nel11 1 0 NA NA NA NA NA NA
## sample_GGACCTA_Nel13 1 0 0 1 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 1 0 0 0
## sample_TCACC_Nel6 0 0 NA NA NA NA NA NA
## sample_TGACCA_Nel1 0 0 NA NA NA NA NA NA
## sample_AAAAGTT_Alt12 1 0 1 1 1 0 0 0
## sample_ACAAA_Alt11 1 0 0 0 1 0 0 0
## sample_ACAGTG_Alt3 0 0 0 1 0 0 0 1
## sample_AGCCC_Alt13 0 0 0 0 1 0 1 0
## sample_ATCACG_Alt5 1 0 0 1 1 0 0 0
## sample_ATCACG_Alt7 1 0 NA NA NA NA NA NA
## sample_CGATGT_Alt1 0 0 0 1 0 0 0 0
## sample_CTGTA_Alt14 1 0 0 0 1 1 1 0
## sample_CTTGA_Alt10 1 0 NA NA NA NA NA NA
## sample_GAATTCA_Alt15 0 0 NA NA NA NA NA NA
## sample_GCCAAT_Alt4 0 0 NA NA NA NA NA NA
## sample_GCCAAT_Alt9 0 0 NA NA NA NA NA NA
## sample_TTAGGC_Alt2 0 0 0 1 0 0 0 1
## sample_TTAGGC_Alt6 1 0 1 0 1 0 0 0
## sample_TTAGGC_Alt8 1 0 NA NA NA NA NA NA
## sample_AAAAGTT_Sub15 NA 0 0 0 1 0 0 0
## sample_ACAAA_Sub1 0 0 NA NA NA NA NA NA
## sample_ACTAT_Sub7 1 0 0 1 0 0 0 1
## sample_AGCAT_Sub13 1 0 0 0 1 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 1 0 0 0
## sample_CGATGT_Sub6 1 0 NA NA NA NA NA NA
## sample_CTTGCTT_Sub14 0 0 0 0 1 0 0 0
## sample_GAATTCA_Sub9 1 0 0 1 0 0 0 1
## sample_GGACCTA_Sub10 1 0 0 0 1 0 0 0
## sample_GTATT_Sub12 0 0 NA NA NA NA NA NA
## sample_TGACCA_Sub2 0 0 NA NA NA NA NA NA
## sample_ACAGTG_Cau2 0 1 0 1 0 0 0 1
## sample_ACAGTG_Cau3 0 1 0 0 1 0 0 0
## sample_ACTAT_Cau11 0 1 NA NA NA NA NA NA
## sample_ACTAT_Cau9 0 1 NA NA NA NA NA NA
## sample_AGCCC_Cau7 0 1 0 0 1 0 1 0
## sample_ATGAAAC_Cau12 0 1 NA NA NA NA NA NA
## sample_CTAGC_Cau5 0 1 NA NA NA NA NA NA
## sample_CTGTA_Cau8 NA 1 0 0 1 0 1 0
## sample_GGACCTA_Cau13 0 1 NA NA NA NA NA NA
## sample_TCACC_Cau1 0 1 0 NA NA 0 0 0
## sample_TCACC_Cau4 0 1 0 0 1 0 1 0
## sample_TGACCA_Cau6 0 1 0 1 1 0 0 0
## sample_AAAAGTT_Div12 0 1 0 1 0 0 0 1
## sample_AAAAGTT_Div13 0 1 NA NA NA NA NA NA
## sample_ACTAT_Div14 0 1 NA NA NA NA NA NA
## sample_AGCAT_Div11 0 1 0 0 1 0 0 0
## sample_AGCCC_Div9 0 1 NA NA NA NA NA NA
## sample_ATCACG_Div1 0 1 0 1 1 0 0 0
## sample_ATGAAAC_Div8 0 1 0 0 1 0 1 0
## sample_CGATGT_Div3 0 1 0 1 0 0 0 1
## sample_CTAGC_Div2 0 1 0 1 1 0 0 0
## sample_CTTGA_Div6 0 1 0 1 1 0 0 0
## sample_CTTGCTT_Div15 0 1 NA NA NA NA NA NA
## sample_GTATT_Div10 0 1 0 1 0 0 0 1
## sample_GTATT_Div7 0 1 NA NA NA NA NA NA
## sample_TGACCA_Div5 0 1 NA NA NA NA NA NA
## sample_TTAGGC_Div4 0 1 NA NA NA NA NA NA
## [,718] [,719] [,720] [,721] [,722] [,723] [,724] [,725]
## sample_ACAAA_Nel3 0 0 0 1 0 0 0 0
## sample_ACAGTG_Nel5 0 0 1 0 0 0 0 0
## sample_AGCAT_Nel8 1 0 0 1 1 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 1 0 0 0 0 0
## sample_CGATGT_Nel4 NA NA NA NA NA 0 0 0
## sample_CTAGC_Nel7 NA NA NA NA NA 0 0 0
## sample_CTGTA_Nel12 0 0 0 1 0 0 0 0
## sample_CTGTA_Nel9 0 0 1 0 0 0 0 0
## sample_CTTGA_Nel2 1 0 0 1 1 0 0 0
## sample_GGACCTA_Nel11 NA NA NA NA NA 0 0 0
## sample_GGACCTA_Nel13 0 0 0 1 0 0 0 0
## sample_GTATT_Nel14 0 0 1 0 0 0 0 0
## sample_TCACC_Nel6 NA NA NA NA NA 0 0 0
## sample_TGACCA_Nel1 NA NA NA NA NA 0 0 0
## sample_AAAAGTT_Alt12 1 0 0 1 0 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 0 0 0 0
## sample_ACAGTG_Alt3 1 0 0 1 1 0 0 0
## sample_AGCCC_Alt13 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt7 NA NA NA NA NA 0 0 0
## sample_CGATGT_Alt1 0 0 0 1 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 NA NA NA NA NA 0 0 0
## sample_GAATTCA_Alt15 NA NA NA NA NA 0 0 0
## sample_GCCAAT_Alt4 NA NA NA NA NA 0 0 0
## sample_GCCAAT_Alt9 NA NA NA NA NA 0 1 0
## sample_TTAGGC_Alt2 1 0 0 1 1 0 0 0
## sample_TTAGGC_Alt6 0 0 1 0 0 0 0 NA
## sample_TTAGGC_Alt8 NA NA NA NA NA 0 0 0
## sample_AAAAGTT_Sub15 0 1 1 0 0 0 0 1
## sample_ACAAA_Sub1 NA NA NA NA NA 0 0 0
## sample_ACTAT_Sub7 1 0 0 1 1 1 0 0
## sample_AGCAT_Sub13 0 0 1 0 0 0 0 0
## sample_AGCCC_Sub11 0 1 1 0 0 0 0 0
## sample_CGATGT_Sub6 NA NA NA NA NA 0 0 0
## sample_CTTGCTT_Sub14 0 1 1 0 0 0 0 1
## sample_GAATTCA_Sub9 1 0 0 1 1 0 0 0
## sample_GGACCTA_Sub10 0 1 1 0 0 0 0 0
## sample_GTATT_Sub12 NA NA NA NA NA 0 0 1
## sample_TGACCA_Sub2 NA NA NA NA NA 0 0 0
## sample_ACAGTG_Cau2 1 1 1 1 0 0 0 1
## sample_ACAGTG_Cau3 0 0 1 0 0 1 0 0
## sample_ACTAT_Cau11 NA NA NA NA NA 1 0 NA
## sample_ACTAT_Cau9 NA NA NA NA NA 1 0 0
## sample_AGCCC_Cau7 0 0 1 0 0 1 0 0
## sample_ATGAAAC_Cau12 NA NA NA NA NA 1 0 NA
## sample_CTAGC_Cau5 NA NA NA NA NA 1 0 1
## sample_CTGTA_Cau8 0 1 1 0 0 NA NA 1
## sample_GGACCTA_Cau13 NA NA NA NA NA NA 0 1
## sample_TCACC_Cau1 0 0 1 0 0 1 0 1
## sample_TCACC_Cau4 0 0 1 0 0 0 0 1
## sample_TGACCA_Cau6 0 0 1 0 0 1 0 1
## sample_AAAAGTT_Div12 1 0 0 1 1 0 0 NA
## sample_AAAAGTT_Div13 NA NA NA NA NA 1 0 1
## sample_ACTAT_Div14 NA NA NA NA NA 0 0 1
## sample_AGCAT_Div11 0 0 1 0 0 1 0 1
## sample_AGCCC_Div9 NA NA NA NA NA 0 NA 1
## sample_ATCACG_Div1 0 0 1 0 0 1 0 1
## sample_ATGAAAC_Div8 0 0 1 0 0 1 0 NA
## sample_CGATGT_Div3 1 0 0 1 1 1 0 1
## sample_CTAGC_Div2 0 0 1 0 0 0 0 1
## sample_CTTGA_Div6 0 0 1 0 0 0 0 1
## sample_CTTGCTT_Div15 NA NA NA NA NA 0 0 NA
## sample_GTATT_Div10 1 0 0 1 1 1 0 NA
## sample_GTATT_Div7 NA NA NA NA NA 1 0 NA
## sample_TGACCA_Div5 NA NA NA NA NA 0 0 1
## sample_TTAGGC_Div4 NA NA NA NA NA 1 0 0
## [,726] [,727] [,728] [,729] [,730] [,731] [,732] [,733]
## sample_ACAAA_Nel3 0 0 0 0 0 1 1 0
## sample_ACAGTG_Nel5 0 1 0 0 0 1 1 0
## sample_AGCAT_Nel8 0 0 0 0 0 1 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 1 0 0 0 1 0 0
## sample_CGATGT_Nel4 0 1 0 0 0 1 0 0
## sample_CTAGC_Nel7 0 1 0 0 0 0 1 0
## sample_CTGTA_Nel12 0 1 0 0 0 1 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 1 0
## sample_CTTGA_Nel2 0 1 0 0 0 1 1 0
## sample_GGACCTA_Nel11 0 1 0 0 0 1 1 0
## sample_GGACCTA_Nel13 0 1 0 0 0 0 0 0
## sample_GTATT_Nel14 0 1 0 0 0 0 1 0
## sample_TCACC_Nel6 0 0 0 0 0 1 1 0
## sample_TGACCA_Nel1 0 1 0 0 0 0 1 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 1 0
## sample_ACAAA_Alt11 0 1 0 0 0 1 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 1 0 0
## sample_AGCCC_Alt13 0 1 0 0 0 1 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 1 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 1 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 1 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 1 0 0 0 1 0 0
## sample_GAATTCA_Alt15 0 1 0 0 0 1 0 0
## sample_GCCAAT_Alt4 0 1 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 1 1 0
## sample_TTAGGC_Alt2 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt6 NA NA NA NA NA 0 0 0
## sample_TTAGGC_Alt8 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 1 0 0 1 1 NA NA NA
## sample_ACAAA_Sub1 0 1 0 0 0 1 0 0
## sample_ACTAT_Sub7 0 1 0 0 0 1 0 0
## sample_AGCAT_Sub13 0 1 0 0 0 1 0 0
## sample_AGCCC_Sub11 0 1 0 0 0 NA NA NA
## sample_CGATGT_Sub6 0 1 1 0 0 NA NA NA
## sample_CTTGCTT_Sub14 1 1 0 0 0 1 0 0
## sample_GAATTCA_Sub9 0 1 0 0 0 1 0 0
## sample_GGACCTA_Sub10 0 1 0 0 0 0 1 0
## sample_GTATT_Sub12 1 0 0 1 1 0 0 0
## sample_TGACCA_Sub2 0 1 0 0 0 1 0 0
## sample_ACAGTG_Cau2 1 1 0 1 0 0 0 NA
## sample_ACAGTG_Cau3 0 1 0 0 0 0 0 1
## sample_ACTAT_Cau11 NA NA NA NA NA 0 0 1
## sample_ACTAT_Cau9 0 1 1 0 0 0 0 1
## sample_AGCCC_Cau7 0 1 0 0 0 0 0 1
## sample_ATGAAAC_Cau12 NA NA NA NA NA 0 0 1
## sample_CTAGC_Cau5 1 1 0 1 1 0 0 1
## sample_CTGTA_Cau8 1 1 0 1 1 0 0 NA
## sample_GGACCTA_Cau13 1 1 0 1 1 NA NA 1
## sample_TCACC_Cau1 1 1 0 1 0 0 0 1
## sample_TCACC_Cau4 1 1 0 0 0 0 0 1
## sample_TGACCA_Cau6 1 1 0 0 1 0 0 1
## sample_AAAAGTT_Div12 NA NA NA NA NA 0 0 1
## sample_AAAAGTT_Div13 1 1 0 1 0 0 0 1
## sample_ACTAT_Div14 1 1 0 1 1 0 0 1
## sample_AGCAT_Div11 1 1 0 0 0 0 0 1
## sample_AGCCC_Div9 1 1 0 1 1 0 0 1
## sample_ATCACG_Div1 1 1 0 1 0 0 0 1
## sample_ATGAAAC_Div8 NA NA NA NA NA 0 0 1
## sample_CGATGT_Div3 1 1 0 0 0 0 0 1
## sample_CTAGC_Div2 1 1 0 0 0 0 0 1
## sample_CTTGA_Div6 1 1 0 1 0 0 0 1
## sample_CTTGCTT_Div15 NA NA NA NA NA 0 0 1
## sample_GTATT_Div10 NA NA NA NA NA 0 0 1
## sample_GTATT_Div7 NA NA NA NA NA 0 0 1
## sample_TGACCA_Div5 1 1 0 NA 0 0 0 1
## sample_TTAGGC_Div4 0 1 1 0 0 0 0 1
## [,734] [,735] [,736] [,737] [,738] [,739] [,740] [,741]
## sample_ACAAA_Nel3 0 0 1 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 1 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 1 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 1 0 0 0 1 0
## sample_GGACCTA_Nel11 0 0 1 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 NA NA 0 0 0 0 0
## sample_TGACCA_Nel1 0 NA NA 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0 0
## sample_ACAAA_Alt11 0 NA NA 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 1 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 1 NA NA 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 1 0 1 0 0 0
## sample_CGATGT_Alt1 1 0 1 0 0 0 0 0
## sample_CTGTA_Alt14 1 0 1 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 1 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 1 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 1 0 0 0 0 0
## sample_GCCAAT_Alt9 0 NA NA 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA 0 1 0 NA 0
## sample_ACAAA_Sub1 0 NA NA 0 0 0 NA 0
## sample_ACTAT_Sub7 0 0 1 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 NA 0 0 0 0 0
## sample_AGCCC_Sub11 NA NA NA NA NA NA 0 0
## sample_CGATGT_Sub6 NA 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 NA NA 0 0 0 NA 0
## sample_GAATTCA_Sub9 0 1 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA NA 0 NA 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 NA 0
## sample_ACAGTG_Cau2 NA NA NA NA 0 NA 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 1 0 0 NA 0 0
## sample_AGCCC_Cau7 0 NA NA 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 NA 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 NA NA NA 1 1 1 NA 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 NA 0
## sample_TCACC_Cau1 0 NA NA 0 0 0 0 0
## sample_TCACC_Cau4 0 NA NA 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 NA 0 NA 0 1
## sample_ACTAT_Div14 0 0 0 0 NA 0 0 0
## sample_AGCAT_Div11 0 NA NA 0 0 0 0 0
## sample_AGCCC_Div9 0 0 1 0 0 0 0 1
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 NA NA 0 0 0 0 1
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 NA NA 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 NA NA NA 0 1
## sample_CTTGCTT_Div15 0 0 0 0 0 0 NA 1
## sample_GTATT_Div10 0 0 1 0 0 0 0 0
## sample_GTATT_Div7 0 NA NA 0 0 0 0 0
## sample_TGACCA_Div5 0 0 NA NA NA NA 0 0
## sample_TTAGGC_Div4 0 0 1 0 0 0 0 0
## [,742] [,743] [,744] [,745] [,746] [,747] [,748] [,749]
## sample_ACAAA_Nel3 0 0 0 1 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 1 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 1 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 1 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 1 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 1 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 1 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 1 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 1 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 1 0 0 0 0
## sample_GTATT_Nel14 0 0 0 1 0 0 0 0
## sample_TCACC_Nel6 0 0 0 1 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 1 1 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 1 0 0 0 0
## sample_ACAAA_Alt11 0 1 0 1 0 0 0 0
## sample_ACAGTG_Alt3 0 1 0 1 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 1 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 1 0 1 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 1 0 0 0 0
## sample_CTGTA_Alt14 0 1 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 1 0 1 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt2 0 1 0 1 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Sub15 0 1 NA NA 0 NA NA NA
## sample_ACAAA_Sub1 0 1 0 1 0 0 NA NA
## sample_ACTAT_Sub7 0 1 0 1 0 0 0 0
## sample_AGCAT_Sub13 0 1 0 1 0 0 0 0
## sample_AGCCC_Sub11 0 1 0 0 0 0 0 0
## sample_CGATGT_Sub6 NA NA 0 0 0 0 NA NA
## sample_CTTGCTT_Sub14 NA NA 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 1 0 1 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 1 NA 1 0 NA NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 1 0 0 0 0 0 1 1
## sample_ACAGTG_Cau3 NA NA 1 0 0 0 NA NA
## sample_ACTAT_Cau11 1 0 1 0 0 0 0 0
## sample_ACTAT_Cau9 1 0 1 0 0 0 1 1
## sample_AGCCC_Cau7 1 0 0 0 0 0 1 1
## sample_ATGAAAC_Cau12 1 0 0 0 0 0 NA NA
## sample_CTAGC_Cau5 1 0 0 0 0 0 1 1
## sample_CTGTA_Cau8 NA NA 0 0 0 0 NA NA
## sample_GGACCTA_Cau13 1 0 1 0 0 0 1 1
## sample_TCACC_Cau1 1 0 0 0 0 0 1 1
## sample_TCACC_Cau4 1 0 0 0 0 0 1 1
## sample_TGACCA_Cau6 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 1 0 0 0 0 0 1 1
## sample_AAAAGTT_Div13 1 0 1 0 0 0 1 1
## sample_ACTAT_Div14 1 0 0 0 0 0 1 1
## sample_AGCAT_Div11 1 0 1 0 0 0 1 1
## sample_AGCCC_Div9 1 0 0 0 0 1 0 0
## sample_ATCACG_Div1 1 0 1 0 0 0 0 0
## sample_ATGAAAC_Div8 1 0 1 0 0 0 1 1
## sample_CGATGT_Div3 1 0 1 0 0 0 1 1
## sample_CTAGC_Div2 1 0 1 0 0 0 1 1
## sample_CTTGA_Div6 0 0 1 0 0 1 1 1
## sample_CTTGCTT_Div15 1 0 0 0 0 0 1 1
## sample_GTATT_Div10 NA NA 1 0 0 0 1 1
## sample_GTATT_Div7 1 0 1 0 0 0 1 1
## sample_TGACCA_Div5 1 0 0 0 0 0 1 1
## sample_TTAGGC_Div4 1 0 0 0 0 0 0 0
## [,750] [,751] [,752] [,753] [,754] [,755] [,756] [,757]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 1 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 1 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 1 0 0 0 0 0
## sample_CTGTA_Nel9 0 1 1 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 1 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 1 0 0 0 0 1
## sample_AAAAGTT_Alt12 0 1 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 1 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 1 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 0 1
## sample_ATCACG_Alt7 0 0 1 0 0 0 0 NA
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 1 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 1
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 NA 0 NA NA NA
## sample_ACAAA_Sub1 0 0 1 NA 0 NA NA NA
## sample_ACTAT_Sub7 0 1 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 1 0 0 NA 0 0 0
## sample_CGATGT_Sub6 0 0 1 NA 0 NA NA NA
## sample_CTTGCTT_Sub14 0 0 NA NA NA 0 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 1 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 NA 0 0 0
## sample_TGACCA_Sub2 0 0 NA 0 NA 0 0 0
## sample_ACAGTG_Cau2 0 0 0 1 NA NA NA 0
## sample_ACAGTG_Cau3 0 0 0 NA 0 1 0 0
## sample_ACTAT_Cau11 0 0 0 1 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 1 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 NA NA NA NA 0
## sample_ATGAAAC_Cau12 1 0 0 NA NA 0 0 0
## sample_CTAGC_Cau5 0 0 0 1 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 NA NA NA NA 0
## sample_GGACCTA_Cau13 0 0 0 1 0 1 1 0
## sample_TCACC_Cau1 0 0 0 1 0 1 0 0
## sample_TCACC_Cau4 0 0 NA 1 0 1 0 0
## sample_TGACCA_Cau6 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 1 0 NA NA 0
## sample_AAAAGTT_Div13 0 0 0 1 0 NA NA 0
## sample_ACTAT_Div14 0 0 0 1 0 1 0 0
## sample_AGCAT_Div11 0 0 0 1 0 NA NA NA
## sample_AGCCC_Div9 0 0 0 1 NA 0 0 0
## sample_ATCACG_Div1 0 0 0 1 0 1 0 0
## sample_ATGAAAC_Div8 0 0 0 1 0 NA NA 0
## sample_CGATGT_Div3 0 0 0 1 1 0 0 0
## sample_CTAGC_Div2 0 0 0 NA 0 NA NA 0
## sample_CTTGA_Div6 0 0 0 1 0 1 0 0
## sample_CTTGCTT_Div15 0 0 0 1 0 NA NA 0
## sample_GTATT_Div10 1 0 0 1 0 NA NA NA
## sample_GTATT_Div7 0 0 0 1 0 0 0 0
## sample_TGACCA_Div5 0 0 0 1 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 1 0 0 0 0
## [,758] [,759] [,760] [,761] [,762] [,763] [,764] [,765]
## sample_ACAAA_Nel3 0 0 0 0 0 1 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 1 0 1
## sample_AGCAT_Nel8 0 0 0 0 0 1 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 1 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 1 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 1 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 1 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 1 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 1 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 1 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 1 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 1 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 NA NA NA NA 0 0 NA 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 1 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 1 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 1 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA 0 0 0 0
## sample_ACAAA_Sub1 NA NA NA NA 0 NA 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 NA 0 0 0
## sample_CGATGT_Sub6 NA NA NA NA NA 0 0 0
## sample_CTTGCTT_Sub14 NA NA NA NA NA 0 1 0
## sample_GAATTCA_Sub9 0 0 0 0 1 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 1 0 0
## sample_GTATT_Sub12 0 0 0 0 NA 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 1 0 1 0 0 0 1 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 1 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 1 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 1 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 1 0
## sample_CTGTA_Cau8 0 0 0 0 0 NA 1 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 1 0
## sample_TCACC_Cau1 0 0 0 0 0 0 1 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 1 0
## sample_ACTAT_Div14 0 0 0 0 0 0 NA 0
## sample_AGCAT_Div11 NA NA NA NA 0 0 1 0
## sample_AGCCC_Div9 0 0 0 0 0 0 1 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 1 0
## sample_CGATGT_Div3 0 0 0 0 0 0 1 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 NA 0
## sample_GTATT_Div10 NA NA NA NA 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 1 1 1 1 0 0 1 0
## [,766] [,767] [,768] [,769] [,770] [,771] [,772] [,773]
## sample_ACAAA_Nel3 1 1 1 1 1 0 0 1
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 1 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel15 1 1 1 1 1 0 0 0
## sample_CGATGT_Nel4 1 1 1 1 1 0 0 0
## sample_CTAGC_Nel7 1 0 0 0 1 0 0 1
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 1 1 1 1 1 0 0 1
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 1 0 0 0 1 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 1 0 0 1
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 1 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 1 0 0 0
## sample_AAAAGTT_Alt12 1 0 0 0 1 0 1 1
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 1 0 0 0 1 0 0 1
## sample_AGCCC_Alt13 0 0 0 0 1 0 0 1
## sample_ATCACG_Alt5 1 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 NA NA NA NA NA 0 0 1
## sample_CTTGA_Alt10 0 0 0 0 1 0 0 0
## sample_GAATTCA_Alt15 NA NA NA NA NA 0 0 1
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 1 1 1 1 1 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 1 0 0 1
## sample_TTAGGC_Alt6 1 1 1 1 1 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 1 0 0 1
## sample_AAAAGTT_Sub15 1 0 0 0 1 NA NA NA
## sample_ACAAA_Sub1 NA NA NA NA NA 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 1 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 NA NA NA NA NA 0 0 0
## sample_CGATGT_Sub6 NA NA NA NA NA 0 0 1
## sample_CTTGCTT_Sub14 NA NA NA NA NA 0 0 NA
## sample_GAATTCA_Sub9 NA NA NA NA NA 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 1 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 0 0 NA
## sample_TGACCA_Sub2 1 1 1 1 1 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 NA NA NA NA NA 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 0 0 NA NA 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 1 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 1 0 0
## sample_ACTAT_Div14 0 0 0 0 0 1 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 1 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 NA NA 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 0 0
## sample_GTATT_Div10 0 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 1 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,774] [,775] [,776] [,777] [,778] [,779] [,780] [,781]
## sample_ACAAA_Nel3 0 0 0 1 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 1
## sample_AGCAT_Nel8 0 0 0 1 1 0 0 1
## sample_ATGAAAC_Nel10 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 1
## sample_CGATGT_Nel4 0 0 1 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 1 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 1 0 0 0 1
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 1
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 1 1 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 1
## sample_TGACCA_Nel1 0 0 0 1 0 0 0 1
## sample_AAAAGTT_Alt12 0 0 1 1 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 1 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 1 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 1 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 1 0 0 0 0 1
## sample_GAATTCA_Alt15 1 0 0 1 0 0 0 1
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 1 1 0 0 0 1
## sample_TTAGGC_Alt2 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt6 0 0 1 1 0 0 0 0
## sample_TTAGGC_Alt8 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA 0 0 0
## sample_ACAAA_Sub1 0 0 1 0 0 NA NA 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 1
## sample_AGCAT_Sub13 0 0 1 0 0 0 0 1
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 1
## sample_CGATGT_Sub6 NA 0 0 0 0 0 0 1
## sample_CTTGCTT_Sub14 NA NA 0 0 0 0 0 1
## sample_GAATTCA_Sub9 0 0 1 0 0 0 0 1
## sample_GGACCTA_Sub10 0 0 1 0 0 0 0 1
## sample_GTATT_Sub12 0 NA NA 0 0 0 0 1
## sample_TGACCA_Sub2 0 0 NA 0 0 0 0 1
## sample_ACAGTG_Cau2 0 NA NA 0 0 NA NA NA
## sample_ACAGTG_Cau3 0 NA 0 0 0 1 0 0
## sample_ACTAT_Cau11 0 1 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 1 0 0 0 0 1 0
## sample_AGCCC_Cau7 0 1 0 0 0 NA NA 0
## sample_ATGAAAC_Cau12 0 NA 0 0 0 1 0 NA
## sample_CTAGC_Cau5 0 1 0 0 0 1 0 0
## sample_CTGTA_Cau8 NA NA 0 0 0 1 0 0
## sample_GGACCTA_Cau13 0 1 0 0 0 1 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 1 0 0 0 NA NA NA
## sample_TGACCA_Cau6 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 1 0 0 0 1 0 0
## sample_AAAAGTT_Div13 0 1 0 0 0 0 0 0
## sample_ACTAT_Div14 0 NA 0 0 0 0 1 0
## sample_AGCAT_Div11 0 NA 0 0 0 0 1 0
## sample_AGCCC_Div9 0 1 0 0 0 0 0 0
## sample_ATCACG_Div1 0 1 0 0 0 1 0 0
## sample_ATGAAAC_Div8 0 1 0 0 0 NA NA 0
## sample_CGATGT_Div3 0 1 0 0 0 1 0 0
## sample_CTAGC_Div2 0 1 0 0 0 0 1 0
## sample_CTTGA_Div6 0 1 0 0 0 0 1 0
## sample_CTTGCTT_Div15 0 1 0 NA NA 1 0 0
## sample_GTATT_Div10 0 1 0 0 0 1 0 0
## sample_GTATT_Div7 0 NA 0 0 0 1 0 0
## sample_TGACCA_Div5 0 NA 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 1 0 0 0 0 0 0
## [,782] [,783] [,784] [,785] [,786] [,787] [,788] [,789]
## sample_ACAAA_Nel3 0 0 NA 0 0 0 0 0
## sample_ACAGTG_Nel5 0 1 NA 1 0 0 0 0
## sample_AGCAT_Nel8 0 1 1 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 1 0 0 0 0 1
## sample_ATGAAAC_Nel15 0 0 1 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 1 1 0 0 0 1
## sample_CTAGC_Nel7 0 0 NA 1 0 0 0 0
## sample_CTGTA_Nel12 0 0 1 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 1 0 0 0 0 1
## sample_CTTGA_Nel2 0 0 1 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 1 1 0 0 0 0
## sample_GGACCTA_Nel13 0 0 NA 0 0 0 0 1
## sample_GTATT_Nel14 0 0 1 0 0 0 0 0
## sample_TCACC_Nel6 0 0 NA 0 0 0 0 1
## sample_TGACCA_Nel1 0 0 1 0 0 0 0 1
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0 1
## sample_ACAAA_Alt11 0 0 NA 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 1 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 0 1
## sample_ATCACG_Alt7 0 0 1 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 1 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 1 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 NA 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 1 1 0 0 0 0
## sample_GCCAAT_Alt4 0 0 1 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 NA 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 1 0 NA 0 NA NA
## sample_ACAAA_Sub1 0 0 1 0 NA 0 NA NA
## sample_ACTAT_Sub7 0 0 1 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 1 0 0 0 1 0
## sample_AGCCC_Sub11 0 0 1 0 0 0 0 NA
## sample_CGATGT_Sub6 0 0 1 0 0 0 NA 0
## sample_CTTGCTT_Sub14 0 0 NA 0 NA 0 NA 0
## sample_GAATTCA_Sub9 0 0 1 NA 0 0 1 0
## sample_GGACCTA_Sub10 0 0 1 0 0 0 1 0
## sample_GTATT_Sub12 0 0 NA NA 0 0 0 0
## sample_TGACCA_Sub2 0 0 1 NA 0 0 1 0
## sample_ACAGTG_Cau2 NA NA 1 0 0 0 0 0
## sample_ACAGTG_Cau3 1 0 1 0 0 0 0 0
## sample_ACTAT_Cau11 1 0 1 0 0 0 0 0
## sample_ACTAT_Cau9 1 0 1 0 0 1 0 0
## sample_AGCCC_Cau7 1 0 1 0 0 1 0 0
## sample_ATGAAAC_Cau12 NA NA NA 0 0 0 0 0
## sample_CTAGC_Cau5 1 0 1 0 0 0 0 0
## sample_CTGTA_Cau8 1 0 NA 0 NA 0 NA 0
## sample_GGACCTA_Cau13 1 0 1 0 0 0 0 0
## sample_TCACC_Cau1 1 0 1 0 0 0 0 0
## sample_TCACC_Cau4 NA NA 1 0 0 0 0 0
## sample_TGACCA_Cau6 1 0 1 NA 0 1 0 0
## sample_AAAAGTT_Div12 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 1 0 1 NA 0 0 0 0
## sample_ACTAT_Div14 1 0 1 0 0 1 0 0
## sample_AGCAT_Div11 0 0 1 NA 0 NA 0 0
## sample_AGCCC_Div9 1 0 1 0 0 0 0 0
## sample_ATCACG_Div1 1 0 1 NA 0 0 0 0
## sample_ATGAAAC_Div8 1 0 1 0 0 0 0 0
## sample_CGATGT_Div3 1 0 1 0 0 0 0 0
## sample_CTAGC_Div2 1 0 1 NA 0 1 0 0
## sample_CTTGA_Div6 1 0 1 0 0 1 0 0
## sample_CTTGCTT_Div15 1 0 1 NA 0 0 0 0
## sample_GTATT_Div10 1 0 1 0 0 0 0 0
## sample_GTATT_Div7 0 0 1 0 0 0 0 0
## sample_TGACCA_Div5 1 0 1 NA 0 1 0 0
## sample_TTAGGC_Div4 1 0 1 0 0 1 0 0
## [,790] [,791] [,792] [,793] [,794] [,795] [,796] [,797]
## sample_ACAAA_Nel3 1 1 0 0 1 1 1 0
## sample_ACAGTG_Nel5 1 1 0 0 1 1 NA 0
## sample_AGCAT_Nel8 1 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel15 1 0 0 0 0 1 0 0
## sample_CGATGT_Nel4 1 0 0 0 1 0 1 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 1 0 0 0 1 0 0 0
## sample_CTGTA_Nel9 1 0 0 0 1 0 1 0
## sample_CTTGA_Nel2 1 0 0 0 1 0 0 0
## sample_GGACCTA_Nel11 1 0 1 0 0 0 1 0
## sample_GGACCTA_Nel13 0 0 0 0 1 1 1 0
## sample_GTATT_Nel14 1 1 0 0 1 0 NA 0
## sample_TCACC_Nel6 1 0 0 0 1 1 1 0
## sample_TGACCA_Nel1 1 0 0 0 1 0 1 0
## sample_AAAAGTT_Alt12 1 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 1 0 0 0 1 0 1 0
## sample_ACAGTG_Alt3 0 0 0 0 1 0 0 0
## sample_AGCCC_Alt13 1 0 0 0 1 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 1 NA 0
## sample_ATCACG_Alt7 1 0 0 0 1 0 NA 0
## sample_CGATGT_Alt1 1 0 0 0 1 1 NA 0
## sample_CTGTA_Alt14 0 0 0 0 0 1 NA 0
## sample_CTTGA_Alt10 0 0 0 0 1 0 1 0
## sample_GAATTCA_Alt15 1 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 1 0 0 0 0 1 NA 0
## sample_GCCAAT_Alt9 1 0 0 0 1 1 NA 0
## sample_TTAGGC_Alt2 1 0 0 0 1 1 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt8 1 0 0 0 1 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA 0 NA 0 NA NA
## sample_ACAAA_Sub1 NA NA NA 0 0 NA NA NA
## sample_ACTAT_Sub7 1 0 0 0 0 1 0 0
## sample_AGCAT_Sub13 1 0 0 0 0 1 0 0
## sample_AGCCC_Sub11 NA NA NA 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 NA 0 NA 0 0
## sample_CTTGCTT_Sub14 0 0 0 NA 0 NA 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 1 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 NA NA NA NA
## sample_TGACCA_Sub2 1 1 0 NA 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 NA NA NA NA 0
## sample_ACAGTG_Cau3 0 0 0 1 0 0 0 0
## sample_ACTAT_Cau11 NA NA NA 1 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 1 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Cau12 NA NA NA 1 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 1 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 1 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 1 0 0 0 0
## sample_TCACC_Cau1 0 0 0 1 0 0 0 0
## sample_TCACC_Cau4 0 0 0 1 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 1 0 0 0 0
## sample_ACTAT_Div14 0 0 0 1 0 0 0 0
## sample_AGCAT_Div11 0 0 0 1 NA NA 0 0
## sample_AGCCC_Div9 0 0 0 1 0 0 0 0
## sample_ATCACG_Div1 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 1 0 0 0 0
## sample_CGATGT_Div3 0 0 0 1 0 0 0 0
## sample_CTAGC_Div2 0 0 0 1 0 0 0 0
## sample_CTTGA_Div6 0 0 0 1 0 0 0 1
## sample_CTTGCTT_Div15 0 0 0 1 NA 0 0 0
## sample_GTATT_Div10 0 0 0 1 NA 0 0 1
## sample_GTATT_Div7 0 0 0 1 NA 0 0 0
## sample_TGACCA_Div5 0 0 0 1 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 1 0 0 0 0
## [,798] [,799] [,800] [,801] [,802] [,803] [,804] [,805]
## sample_ACAAA_Nel3 0 0 0 0 1 0 0 1
## sample_ACAGTG_Nel5 0 0 0 1 1 0 0 1
## sample_AGCAT_Nel8 0 0 0 0 1 0 1 1
## sample_ATGAAAC_Nel10 0 0 0 0 1 0 0 1
## sample_ATGAAAC_Nel15 0 0 0 0 1 0 0 1
## sample_CGATGT_Nel4 0 0 0 1 1 0 0 1
## sample_CTAGC_Nel7 0 0 0 0 1 0 0 1
## sample_CTGTA_Nel12 0 0 0 0 1 0 0 1
## sample_CTGTA_Nel9 0 0 0 0 1 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 1 0 0 1
## sample_GGACCTA_Nel11 0 0 0 0 1 0 0 1
## sample_GGACCTA_Nel13 0 0 0 0 1 0 0 1
## sample_GTATT_Nel14 0 0 0 1 1 0 0 1
## sample_TCACC_Nel6 0 0 0 0 1 0 0 1
## sample_TGACCA_Nel1 0 0 0 0 1 0 0 1
## sample_AAAAGTT_Alt12 0 0 0 1 1 0 0 1
## sample_ACAAA_Alt11 0 0 0 0 1 0 0 1
## sample_ACAGTG_Alt3 0 0 0 1 1 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 1 0 0 1
## sample_ATCACG_Alt5 0 0 0 0 1 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 1 0 0 1
## sample_CGATGT_Alt1 0 0 0 0 1 0 0 1
## sample_CTGTA_Alt14 0 0 0 0 1 0 0 1
## sample_CTTGA_Alt10 0 0 0 0 1 0 0 1
## sample_GAATTCA_Alt15 0 0 0 1 1 0 0 1
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 1
## sample_GCCAAT_Alt9 0 0 0 0 1 0 0 1
## sample_TTAGGC_Alt2 0 0 0 0 1 0 0 1
## sample_TTAGGC_Alt6 0 0 0 0 1 0 0 1
## sample_TTAGGC_Alt8 0 0 0 1 1 0 0 1
## sample_AAAAGTT_Sub15 NA NA NA NA NA NA NA NA
## sample_ACAAA_Sub1 NA NA 0 NA NA NA NA NA
## sample_ACTAT_Sub7 0 0 0 1 1 0 0 1
## sample_AGCAT_Sub13 0 0 0 0 1 0 0 0
## sample_AGCCC_Sub11 0 0 0 1 1 0 0 1
## sample_CGATGT_Sub6 0 0 0 0 NA NA NA NA
## sample_CTTGCTT_Sub14 NA NA 0 1 NA NA NA NA
## sample_GAATTCA_Sub9 0 0 0 0 1 0 0 1
## sample_GGACCTA_Sub10 0 0 0 1 1 0 0 0
## sample_GTATT_Sub12 NA NA 0 NA 1 0 0 1
## sample_TGACCA_Sub2 0 0 0 1 1 0 0 1
## sample_ACAGTG_Cau2 1 NA NA 0 0 1 0 0
## sample_ACAGTG_Cau3 1 0 0 0 0 1 0 0
## sample_ACTAT_Cau11 1 0 0 0 0 1 0 0
## sample_ACTAT_Cau9 1 1 0 0 0 1 0 0
## sample_AGCCC_Cau7 1 0 NA 0 0 1 0 0
## sample_ATGAAAC_Cau12 1 0 NA 0 0 1 0 0
## sample_CTAGC_Cau5 1 0 1 0 0 1 0 0
## sample_CTGTA_Cau8 NA NA NA 0 NA NA NA NA
## sample_GGACCTA_Cau13 0 1 0 0 0 NA NA NA
## sample_TCACC_Cau1 1 1 0 0 0 1 0 0
## sample_TCACC_Cau4 1 0 NA 0 0 1 0 0
## sample_TGACCA_Cau6 1 0 0 0 0 1 0 0
## sample_AAAAGTT_Div12 NA NA 0 0 0 1 0 0
## sample_AAAAGTT_Div13 1 1 1 0 0 1 0 0
## sample_ACTAT_Div14 1 0 1 0 0 1 0 0
## sample_AGCAT_Div11 NA NA 0 0 0 1 0 0
## sample_AGCCC_Div9 NA NA 0 0 0 1 0 0
## sample_ATCACG_Div1 1 0 0 0 0 1 0 0
## sample_ATGAAAC_Div8 NA NA 0 0 0 1 0 0
## sample_CGATGT_Div3 1 1 1 0 0 1 0 0
## sample_CTAGC_Div2 0 1 1 0 0 1 0 0
## sample_CTTGA_Div6 0 1 1 0 0 1 0 0
## sample_CTTGCTT_Div15 1 0 1 0 0 1 0 0
## sample_GTATT_Div10 1 0 1 0 0 1 0 0
## sample_GTATT_Div7 1 0 1 0 0 1 0 0
## sample_TGACCA_Div5 1 0 1 0 0 1 0 0
## sample_TTAGGC_Div4 1 1 0 0 0 1 0 0
## [,806] [,807] [,808] [,809] [,810] [,811] [,812] [,813]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 1 0 0 0 0 1 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 1 0
## sample_CGATGT_Nel4 0 0 0 0 0 1 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 1 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 1 0 0
## sample_GGACCTA_Nel13 0 0 1 1 0 1 1 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 1 1 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 1 0 0 0 0 1 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 1 0 0
## sample_GCCAAT_Alt4 0 0 1 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 1 1
## sample_TTAGGC_Alt8 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Sub15 NA NA NA NA 0 0 1 0
## sample_ACAAA_Sub1 0 0 NA 0 NA NA NA NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 1 0
## sample_AGCCC_Sub11 0 0 0 0 NA NA 0 0
## sample_CGATGT_Sub6 0 0 0 NA 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 NA 0 NA NA 1 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 1 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 1 0
## sample_GTATT_Sub12 0 NA NA 0 NA NA 1 0
## sample_TGACCA_Sub2 0 0 0 0 NA NA 1 0
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 1 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 NA 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 NA 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 NA 0 0 0 0
## sample_CTGTA_Cau8 NA 0 0 0 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 NA 0 0 0 0
## sample_TCACC_Cau1 0 0 0 1 0 0 0 0
## sample_TCACC_Cau4 0 0 NA NA 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 NA 1 0 0 0 0
## sample_AGCCC_Div9 0 0 0 NA 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 1 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 NA 0 0 0 0 0
## sample_GTATT_Div10 0 0 NA 1 0 0 0 0
## sample_GTATT_Div7 0 0 0 NA 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 1 0 0 0
## [,814] [,815] [,816] [,817] [,818] [,819] [,820] [,821]
## sample_ACAAA_Nel3 0 0 0 1 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 1 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA 0 0 0 0 NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 NA
## sample_CTTGCTT_Sub14 NA 0 0 0 0 NA 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA NA 0 0 0 NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 NA 0 NA
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 1
## sample_ACTAT_Cau11 0 0 0 0 0 0 1 1
## sample_ACTAT_Cau9 1 0 0 0 0 0 0 1
## sample_AGCCC_Cau7 NA 0 0 0 0 0 0 1
## sample_ATGAAAC_Cau12 NA 0 0 0 0 NA 0 1
## sample_CTAGC_Cau5 0 0 0 0 0 1 0 1
## sample_CTGTA_Cau8 NA 0 0 0 0 0 0 NA
## sample_GGACCTA_Cau13 0 0 0 0 0 1 0 1
## sample_TCACC_Cau1 0 0 0 0 0 0 0 1
## sample_TCACC_Cau4 0 NA NA 0 0 0 0 1
## sample_TGACCA_Cau6 0 0 1 0 0 0 0 1
## sample_AAAAGTT_Div12 0 0 0 0 0 NA 0 1
## sample_AAAAGTT_Div13 0 0 0 0 1 0 0 1
## sample_ACTAT_Div14 0 0 0 0 0 1 0 1
## sample_AGCAT_Div11 0 0 0 0 0 0 0 1
## sample_AGCCC_Div9 0 0 0 0 0 0 1 1
## sample_ATCACG_Div1 0 0 0 0 0 NA 1 1
## sample_ATGAAAC_Div8 0 0 1 0 0 NA 0 1
## sample_CGATGT_Div3 0 0 0 0 0 NA 0 1
## sample_CTAGC_Div2 0 0 0 0 0 NA 0 1
## sample_CTTGA_Div6 0 0 0 0 0 1 0 1
## sample_CTTGCTT_Div15 0 0 0 0 0 NA 0 1
## sample_GTATT_Div10 0 0 0 0 0 NA 0 1
## sample_GTATT_Div7 0 0 0 0 0 NA 0 1
## sample_TGACCA_Div5 0 0 0 0 0 0 0 1
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 1
## [,822] [,823] [,824] [,825] [,826] [,827] [,828] [,829]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 1 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 1 1 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 1
## sample_CTAGC_Nel7 0 0 0 0 1 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 1 0 0 NA
## sample_CTGTA_Nel9 0 0 0 0 1 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 1 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 1 0 0 0
## sample_GGACCTA_Nel13 0 1 0 0 1 0 0 0
## sample_GTATT_Nel14 0 0 0 0 1 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 1 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 1 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 1
## sample_CTGTA_Alt14 0 0 0 0 1 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 1 0 0 1
## sample_GAATTCA_Alt15 0 1 0 0 1 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt2 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt8 0 1 0 0 1 0 0 1
## sample_AAAAGTT_Sub15 NA 0 0 0 0 NA 0 0
## sample_ACAAA_Sub1 NA 0 0 0 0 NA 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 NA 0 0
## sample_CGATGT_Sub6 NA 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 NA 0 0
## sample_GAATTCA_Sub9 0 0 0 0 1 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 1 0 0 0
## sample_GTATT_Sub12 NA 0 0 NA NA 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 1
## sample_ACAGTG_Cau2 NA 0 0 0 0 0 0 NA
## sample_ACAGTG_Cau3 1 0 1 1 0 0 0 0
## sample_ACTAT_Cau11 1 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 1 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 1 0 0 0 0 0 0 0
## sample_CTAGC_Cau5 1 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 NA 0 0 0 0 NA 0 0
## sample_GGACCTA_Cau13 1 0 0 0 0 0 0 0
## sample_TCACC_Cau1 1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 1 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 1 0 0 0 0 0 1 0
## sample_ACTAT_Div14 1 0 0 0 0 0 0 0
## sample_AGCAT_Div11 1 0 0 0 0 0 0 0
## sample_AGCCC_Div9 1 0 0 0 0 0 0 0
## sample_ATCACG_Div1 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 1 0 0 0 0 0 0 0
## sample_CGATGT_Div3 1 0 0 0 0 0 0 0
## sample_CTAGC_Div2 1 0 0 0 0 0 0 0
## sample_CTTGA_Div6 1 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 1 0 0 0 0 0 0 0
## sample_GTATT_Div10 1 0 0 0 0 0 0 0
## sample_GTATT_Div7 1 0 0 0 0 0 0 0
## sample_TGACCA_Div5 1 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 1 0 0 0 0 0 0 0
## [,830] [,831] [,832] [,833] [,834] [,835] [,836] [,837]
## sample_ACAAA_Nel3 0 0 0 0 0 0 1 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 1
## sample_CGATGT_Nel4 0 0 0 0 0 0 1 1
## sample_CTAGC_Nel7 0 0 0 0 0 0 1 0
## sample_CTGTA_Nel12 NA 0 0 0 0 0 1 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 1 1
## sample_CTTGA_Nel2 0 0 0 0 0 0 1 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 1 1
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 1
## sample_GTATT_Nel14 0 0 0 1 0 0 0 1
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 1 1
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 1
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 1
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 1 1 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 1 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 1 0
## sample_GAATTCA_Alt15 0 0 0 0 0 1 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 1
## sample_AAAAGTT_Sub15 0 0 0 NA NA 0 NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 0 NA NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 1 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 1 0
## sample_AGCCC_Sub11 0 NA NA 0 0 0 0 NA
## sample_CGATGT_Sub6 0 0 0 0 0 0 NA NA
## sample_CTTGCTT_Sub14 0 0 0 0 0 NA NA 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 1 0
## sample_GGACCTA_Sub10 0 1 1 0 0 0 1 0
## sample_GTATT_Sub12 0 0 0 NA NA 0 1 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 1 0
## sample_ACAGTG_Cau2 NA 1 1 0 0 0 0 0
## sample_ACAGTG_Cau3 0 1 1 0 0 0 0 0
## sample_ACTAT_Cau11 0 1 1 0 0 0 0 0
## sample_ACTAT_Cau9 0 1 1 0 0 0 0 0
## sample_AGCCC_Cau7 0 NA NA 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 1 1 0 0 0 0 0
## sample_CTAGC_Cau5 0 1 1 0 1 0 0 0
## sample_CTGTA_Cau8 0 1 1 0 0 0 NA 0
## sample_GGACCTA_Cau13 0 1 1 0 0 0 0 0
## sample_TCACC_Cau1 0 1 1 0 0 0 0 0
## sample_TCACC_Cau4 0 1 1 0 0 0 0 0
## sample_TGACCA_Cau6 0 1 1 0 0 0 0 0
## sample_AAAAGTT_Div12 0 1 1 0 0 0 0 0
## sample_AAAAGTT_Div13 0 1 1 0 1 0 0 0
## sample_ACTAT_Div14 0 1 1 0 0 0 0 0
## sample_AGCAT_Div11 0 1 1 0 0 0 0 0
## sample_AGCCC_Div9 1 1 1 0 0 0 0 0
## sample_ATCACG_Div1 0 1 1 0 1 0 0 0
## sample_ATGAAAC_Div8 0 1 1 0 0 0 0 0
## sample_CGATGT_Div3 0 1 1 0 1 0 0 0
## sample_CTAGC_Div2 0 1 1 0 1 0 0 0
## sample_CTTGA_Div6 0 1 1 0 0 0 0 0
## sample_CTTGCTT_Div15 0 1 1 0 0 0 0 0
## sample_GTATT_Div10 0 1 1 0 1 0 0 0
## sample_GTATT_Div7 0 1 1 0 0 0 0 0
## sample_TGACCA_Div5 0 1 1 0 0 0 0 0
## sample_TTAGGC_Div4 0 1 1 0 0 0 0 0
## [,838] [,839] [,840] [,841] [,842] [,843] [,844] [,845]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 NA 0
## sample_CTGTA_Nel9 0 NA NA NA NA NA 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 1 0 0 1 0 0
## sample_TCACC_Nel6 0 NA NA NA NA NA 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 1 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 NA NA NA NA NA 0 0
## sample_CTGTA_Alt14 0 NA NA NA NA NA 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 NA NA NA NA NA 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 1 0 0 1 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 NA NA NA NA NA 0 0
## sample_AAAAGTT_Sub15 0 1 1 0 0 1 NA 0
## sample_ACAAA_Sub1 0 NA NA NA NA NA 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 1 1 0 0 0 0 0
## sample_CGATGT_Sub6 0 1 1 0 0 0 0 NA
## sample_CTTGCTT_Sub14 0 1 1 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 1 1 0 0 0 0 0
## sample_GTATT_Sub12 NA 1 1 0 0 0 0 0
## sample_TGACCA_Sub2 0 1 1 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 0 1 1
## sample_ACAGTG_Cau3 0 0 0 0 0 0 1 1
## sample_ACTAT_Cau11 0 0 1 0 0 1 1 1
## sample_ACTAT_Cau9 0 0 0 0 0 0 1 1
## sample_AGCCC_Cau7 0 NA NA NA NA NA 1 1
## sample_ATGAAAC_Cau12 0 1 1 0 0 0 1 1
## sample_CTAGC_Cau5 0 0 1 0 0 NA 1 1
## sample_CTGTA_Cau8 0 0 1 0 0 1 1 1
## sample_GGACCTA_Cau13 0 0 0 0 0 0 1 1
## sample_TCACC_Cau1 0 1 1 0 0 0 1 1
## sample_TCACC_Cau4 NA 1 1 0 0 1 1 1
## sample_TGACCA_Cau6 0 0 1 0 0 1 1 1
## sample_AAAAGTT_Div12 0 0 0 0 0 0 1 1
## sample_AAAAGTT_Div13 0 0 0 0 0 0 1 1
## sample_ACTAT_Div14 0 0 1 0 0 1 1 1
## sample_AGCAT_Div11 0 0 1 0 0 0 1 1
## sample_AGCCC_Div9 0 0 1 0 0 1 1 1
## sample_ATCACG_Div1 0 NA NA NA NA NA 1 1
## sample_ATGAAAC_Div8 0 NA NA NA NA NA 1 1
## sample_CGATGT_Div3 0 0 1 0 0 1 1 1
## sample_CTAGC_Div2 0 1 1 0 0 0 1 1
## sample_CTTGA_Div6 0 0 1 0 0 0 1 1
## sample_CTTGCTT_Div15 0 0 1 0 0 0 1 1
## sample_GTATT_Div10 0 0 1 0 1 0 1 1
## sample_GTATT_Div7 0 0 1 0 0 0 1 1
## sample_TGACCA_Div5 0 0 1 0 0 0 1 1
## sample_TTAGGC_Div4 0 1 1 0 0 0 1 1
## [,846] [,847] [,848] [,849] [,850] [,851] [,852] [,853]
## sample_ACAAA_Nel3 0 0 0 0 0 1 0 0
## sample_ACAGTG_Nel5 0 1 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 1 0 0 0 0 1
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 1 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 1 0 0 0 0 1
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 1 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 1 0 1 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 NA 0 0 0 NA NA
## sample_ACAAA_Sub1 NA NA NA 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 NA 0 0 0 NA NA
## sample_CGATGT_Sub6 NA NA 1 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 NA NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 0 NA NA
## sample_TGACCA_Sub2 0 0 1 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 1 0 0 NA NA
## sample_ACAGTG_Cau3 0 0 0 1 0 0 0 1
## sample_ACTAT_Cau11 0 0 0 1 0 0 0 1
## sample_ACTAT_Cau9 0 0 0 1 0 0 0 1
## sample_AGCCC_Cau7 0 0 0 1 0 0 0 1
## sample_ATGAAAC_Cau12 0 0 0 1 0 0 NA NA
## sample_CTAGC_Cau5 0 0 0 1 1 0 0 1
## sample_CTGTA_Cau8 0 0 0 1 0 0 NA NA
## sample_GGACCTA_Cau13 0 0 0 1 0 0 0 1
## sample_TCACC_Cau1 0 0 0 1 0 0 0 1
## sample_TCACC_Cau4 0 0 0 1 0 0 NA NA
## sample_TGACCA_Cau6 0 0 0 1 0 0 0 1
## sample_AAAAGTT_Div12 0 0 0 1 0 0 0 1
## sample_AAAAGTT_Div13 0 0 0 1 1 0 NA NA
## sample_ACTAT_Div14 0 0 0 1 0 0 0 1
## sample_AGCAT_Div11 0 0 0 1 0 0 0 1
## sample_AGCCC_Div9 0 0 0 1 0 0 0 1
## sample_ATCACG_Div1 0 0 0 1 0 0 0 1
## sample_ATGAAAC_Div8 0 0 0 1 0 0 0 1
## sample_CGATGT_Div3 0 0 0 1 1 0 0 1
## sample_CTAGC_Div2 0 0 0 1 0 0 0 0
## sample_CTTGA_Div6 0 0 0 1 0 0 0 1
## sample_CTTGCTT_Div15 0 0 0 1 0 0 0 1
## sample_GTATT_Div10 0 0 0 1 0 0 NA NA
## sample_GTATT_Div7 0 0 0 1 0 0 0 1
## sample_TGACCA_Div5 0 0 0 1 0 0 NA NA
## sample_TTAGGC_Div4 0 0 0 1 0 0 0 1
## [,854] [,855] [,856] [,857] [,858] [,859] [,860] [,861]
## sample_ACAAA_Nel3 0 1 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 1 0 0 0 0 1 1 1
## sample_CTGTA_Nel9 0 1 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 1 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 1 0 0 0 0 1 1
## sample_ATCACG_Alt5 0 1 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 1 0 0 0 1 1 1
## sample_CGATGT_Alt1 0 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 1 1
## sample_TTAGGC_Alt6 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 NA NA 0 0 0 0
## sample_ACAAA_Sub1 NA 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 1 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 0 0 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 NA NA 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 1 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 NA NA NA 0 0 0 0
## sample_CTAGC_Cau5 0 0 1 0 1 0 0 0
## sample_CTGTA_Cau8 0 0 NA NA 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 1 0 0 0 0 0
## sample_TCACC_Cau4 NA 0 NA NA 0 0 0 0
## sample_TGACCA_Cau6 0 0 1 0 1 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 1 0 0 0 0 0
## sample_ACTAT_Div14 0 0 1 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 NA NA 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 NA 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 1 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 0 0
## sample_GTATT_Div10 NA 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 NA NA 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,862] [,863] [,864] [,865] [,866] [,867] [,868] [,869]
## sample_ACAAA_Nel3 0 0 1 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 1 1 0 0 0 1
## sample_ATGAAAC_Nel15 0 0 0 1 0 0 0 1
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 1 0 0 0 1
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 1 0 0 0 1
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 1 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 1
## sample_AGCCC_Alt13 0 0 0 0 1 0 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 1 0 0 0 1
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 1 0 0 0 1
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 NA 0 0 0 0 0 0
## sample_ACAAA_Sub1 0 NA 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 1 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA 0 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA 0 0 0 0 0 0
## sample_TGACCA_Sub2 1 0 0 1 0 0 0 1
## sample_ACAGTG_Cau2 0 NA 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 NA 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 NA 0 0 0 0 0 0
## sample_GGACCTA_Cau13 0 NA 0 0 0 0 0 0
## sample_TCACC_Cau1 0 1 0 0 0 0 0 0
## sample_TCACC_Cau4 0 NA 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Div13 0 1 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 1 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 NA 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 1 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 NA 0 0 0 0 0 0
## sample_GTATT_Div10 0 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,870] [,871] [,872] [,873] [,874] [,875] [,876] [,877]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 1 0 0 0 1 0 0
## sample_ATGAAAC_Nel10 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 1 0 0 0 0 0 NA NA
## sample_CTGTA_Nel12 0 0 0 0 0 0 NA NA
## sample_CTGTA_Nel9 1 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 1 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 1 0 0 0 0 NA NA
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 1 0 0 0 0 0 NA NA
## sample_AGCCC_Alt13 0 0 0 0 0 0 NA NA
## sample_ATCACG_Alt5 0 1 0 0 0 1 NA NA
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 1 0 0 0 1 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 1 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 NA NA
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 0 0 0 0
## sample_ACAAA_Sub1 0 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 1 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA NA NA NA NA 0 0
## sample_TGACCA_Sub2 1 NA NA NA NA NA 0 0
## sample_ACAGTG_Cau2 0 NA NA NA NA NA 0 0
## sample_ACAGTG_Cau3 0 1 1 0 0 0 0 0
## sample_ACTAT_Cau11 0 1 1 0 0 0 NA NA
## sample_ACTAT_Cau9 0 1 1 0 0 0 0 0
## sample_AGCCC_Cau7 0 NA NA NA NA NA 0 0
## sample_ATGAAAC_Cau12 0 1 1 0 0 0 0 0
## sample_CTAGC_Cau5 0 1 1 0 0 0 0 0
## sample_CTGTA_Cau8 0 NA NA NA NA NA 0 0
## sample_GGACCTA_Cau13 0 1 1 0 0 0 0 0
## sample_TCACC_Cau1 0 1 1 0 0 0 0 0
## sample_TCACC_Cau4 0 NA NA NA NA NA 0 0
## sample_TGACCA_Cau6 0 1 1 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 1 1 0 0 1 1 1
## sample_ACTAT_Div14 0 1 1 0 0 0 NA NA
## sample_AGCAT_Div11 0 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 NA NA NA NA NA NA NA
## sample_ATCACG_Div1 0 1 1 0 0 0 0 0
## sample_ATGAAAC_Div8 0 1 0 0 0 1 0 0
## sample_CGATGT_Div3 0 1 0 0 0 1 0 0
## sample_CTAGC_Div2 0 1 0 0 0 0 0 0
## sample_CTTGA_Div6 0 1 0 0 1 1 NA NA
## sample_CTTGCTT_Div15 0 NA NA NA NA NA 1 1
## sample_GTATT_Div10 0 1 1 0 0 0 NA NA
## sample_GTATT_Div7 0 1 1 0 0 0 0 0
## sample_TGACCA_Div5 0 1 1 0 0 1 NA NA
## sample_TTAGGC_Div4 0 0 0 0 0 0 NA NA
## [,878] [,879] [,880] [,881] [,882] [,883] [,884] [,885]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 NA NA NA NA NA NA 0 0
## sample_CTGTA_Nel12 NA NA NA NA NA NA 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 NA NA NA NA NA NA 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 NA NA NA NA NA NA 0 0
## sample_AGCCC_Alt13 NA NA NA NA NA NA 0 0
## sample_ATCACG_Alt5 NA NA NA NA NA NA 0 1
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 NA NA NA NA NA NA 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 0 0 NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 0 NA NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 1 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 NA
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 NA
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 NA 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 1 0
## sample_GTATT_Sub12 0 0 0 0 0 0 NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 1 0
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 NA NA NA NA NA NA 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 NA
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 0 NA
## sample_CTAGC_Cau5 0 1 0 1 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 0 0 0 0 NA
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 1 0 1 0 1 1 0 0
## sample_ACTAT_Div14 NA NA NA NA NA NA 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0 0
## sample_AGCCC_Div9 NA NA NA NA NA NA 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0
## sample_CTTGA_Div6 NA NA NA NA NA NA 0 0
## sample_CTTGCTT_Div15 1 0 1 0 1 1 0 0
## sample_GTATT_Div10 NA NA NA NA NA NA 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0 0
## sample_TGACCA_Div5 NA NA NA NA NA NA 0 0
## sample_TTAGGC_Div4 NA NA NA NA NA NA 0 0
## [,886] [,887] [,888] [,889] [,890] [,891] [,892] [,893]
## sample_ACAAA_Nel3 0 0 0 0 0 0 1 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Nel10 0 0 0 1 0 1 1 0
## sample_ATGAAAC_Nel15 0 0 0 1 0 1 0 0
## sample_CGATGT_Nel4 0 0 0 1 0 0 1 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 1 1 0 0 1 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 1 0
## sample_CTTGA_Nel2 0 0 0 1 0 0 0 0
## sample_GGACCTA_Nel11 0 0 1 0 1 0 0 0
## sample_GGACCTA_Nel13 0 0 0 1 0 1 1 0
## sample_GTATT_Nel14 0 0 0 0 0 0 1 0
## sample_TCACC_Nel6 0 0 1 0 0 0 1 0
## sample_TGACCA_Nel1 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 1 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 1 0 1 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 1 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 1 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 1 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 1 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 1 0 0 1 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 NA 0 0 0 0 1 0
## sample_AAAAGTT_Sub15 NA NA 0 0 0 NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 NA 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 1 0
## sample_CGATGT_Sub6 NA 0 0 0 0 0 NA NA
## sample_CTTGCTT_Sub14 0 0 1 NA NA 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 1 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 0 NA NA NA NA NA
## sample_TGACCA_Sub2 0 0 1 0 0 0 0 0
## sample_ACAGTG_Cau2 1 NA 0 0 0 0 0 0
## sample_ACAGTG_Cau3 1 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 1 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 1 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 1 1 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 NA 1 0 NA NA NA NA NA
## sample_CTAGC_Cau5 1 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 1 NA 0 0 0 NA NA NA
## sample_GGACCTA_Cau13 1 1 0 0 0 0 0 0
## sample_TCACC_Cau1 1 1 0 0 0 0 0 0
## sample_TCACC_Cau4 1 0 0 NA NA 0 0 0
## sample_TGACCA_Cau6 1 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 1 NA 0 0 0 0 0 0
## sample_AAAAGTT_Div13 1 0 0 0 0 0 0 0
## sample_ACTAT_Div14 1 0 0 0 0 0 0 0
## sample_AGCAT_Div11 1 0 0 0 0 0 0 0
## sample_AGCCC_Div9 1 0 0 0 0 0 0 0
## sample_ATCACG_Div1 1 NA 0 0 0 0 0 0
## sample_ATGAAAC_Div8 1 NA 0 0 0 0 NA NA
## sample_CGATGT_Div3 1 0 0 0 0 0 0 0
## sample_CTAGC_Div2 1 0 0 0 0 0 0 0
## sample_CTTGA_Div6 1 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 1 NA 0 0 0 0 0 0
## sample_GTATT_Div10 1 NA 0 0 0 0 0 1
## sample_GTATT_Div7 1 NA 0 0 0 0 NA NA
## sample_TGACCA_Div5 1 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 1 0 0 0 0 0 0 1
## [,894] [,895] [,896] [,897] [,898] [,899] [,900] [,901]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 1 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 1 0 0 0 0 0 0
## sample_TCACC_Nel6 0 1 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 1 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 1 0 0 0 0
## sample_ACAGTG_Alt3 0 1 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 1 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 1 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 1 0 0 0 1 0 0
## sample_CGATGT_Alt1 0 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 1 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 1 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 1 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 1 0 0
## sample_TTAGGC_Alt6 1 1 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA 0 NA NA 0 NA
## sample_ACAAA_Sub1 0 0 NA 0 NA NA 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 NA 0 NA 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 NA NA 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 0 NA NA NA NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 NA 0 0 NA NA
## sample_ACAGTG_Cau3 0 0 0 0 NA NA 1 1
## sample_ACTAT_Cau11 0 0 0 0 1 0 1 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 1 0
## sample_AGCCC_Cau7 0 0 0 0 NA NA 1 1
## sample_ATGAAAC_Cau12 NA 0 0 0 0 0 1 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 1 1
## sample_CTGTA_Cau8 NA 0 0 0 NA NA NA 0
## sample_GGACCTA_Cau13 0 0 0 0 NA NA 1 0
## sample_TCACC_Cau1 0 0 0 0 0 0 NA 1
## sample_TCACC_Cau4 0 0 0 0 0 0 1 0
## sample_TGACCA_Cau6 0 0 0 0 NA NA 1 0
## sample_AAAAGTT_Div12 0 0 0 0 1 0 1 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 1 NA
## sample_ACTAT_Div14 0 0 0 0 0 0 1 0
## sample_AGCAT_Div11 0 0 0 NA 0 0 1 0
## sample_AGCCC_Div9 0 0 0 0 0 0 1 1
## sample_ATCACG_Div1 0 0 0 0 0 0 1 0
## sample_ATGAAAC_Div8 NA 0 0 0 0 0 1 0
## sample_CGATGT_Div3 0 0 0 0 0 0 1 0
## sample_CTAGC_Div2 0 0 0 0 0 0 1 0
## sample_CTTGA_Div6 0 0 0 0 0 0 1 1
## sample_CTTGCTT_Div15 0 0 0 NA 0 0 1 0
## sample_GTATT_Div10 0 0 0 NA 0 0 1 NA
## sample_GTATT_Div7 NA 0 0 0 0 0 NA NA
## sample_TGACCA_Div5 0 0 0 0 0 0 1 0
## sample_TTAGGC_Div4 0 0 0 0 1 0 1 1
## [,902] [,903] [,904] [,905] [,906] [,907] [,908] [,909]
## sample_ACAAA_Nel3 0 0 1 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 1 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 1 0
## sample_CGATGT_Nel4 0 0 0 0 1 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 1 0 1 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 1 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 1 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 1 0 0 0 0 0
## sample_GTATT_Nel14 0 0 1 0 0 0 0 0
## sample_TCACC_Nel6 0 0 1 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 1 0 0 0
## sample_ACAGTG_Alt3 0 0 1 0 1 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 1 NA NA 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 1 0 0 0
## sample_CTTGA_Alt10 0 0 1 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 1 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 1 0 1 0 0 0
## sample_TTAGGC_Alt8 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 NA NA 0 0 0 NA NA
## sample_ACAAA_Sub1 0 0 1 0 0 0 NA 0
## sample_ACTAT_Sub7 0 0 1 0 1 0 0 0
## sample_AGCAT_Sub13 0 0 1 0 0 0 0 0
## sample_AGCCC_Sub11 NA 1 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 NA 0 0 0 NA NA
## sample_CTTGCTT_Sub14 NA 0 NA 0 0 0 0 NA
## sample_GAATTCA_Sub9 0 0 1 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 0 0 0 0 NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA NA 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 1 0 1 0 0 0 0
## sample_ACTAT_Cau11 0 1 0 1 0 0 0 1
## sample_ACTAT_Cau9 1 1 0 1 0 0 0 0
## sample_AGCCC_Cau7 0 1 0 1 0 0 0 0
## sample_ATGAAAC_Cau12 1 1 0 1 0 0 0 0
## sample_CTAGC_Cau5 1 1 0 1 0 0 0 0
## sample_CTGTA_Cau8 1 NA 0 1 0 0 NA 0
## sample_GGACCTA_Cau13 NA 1 0 1 0 0 0 1
## sample_TCACC_Cau1 1 NA 0 1 0 0 0 0
## sample_TCACC_Cau4 NA 1 0 1 0 0 NA 0
## sample_TGACCA_Cau6 1 1 0 1 0 0 0 1
## sample_AAAAGTT_Div12 1 1 0 1 0 0 0 0
## sample_AAAAGTT_Div13 NA 1 0 1 0 0 0 1
## sample_ACTAT_Div14 1 1 0 1 0 0 0 1
## sample_AGCAT_Div11 0 1 0 1 0 0 0 0
## sample_AGCCC_Div9 0 1 0 1 0 0 0 0
## sample_ATCACG_Div1 1 1 0 1 0 0 0 1
## sample_ATGAAAC_Div8 1 1 0 1 0 0 0 0
## sample_CGATGT_Div3 1 1 0 1 0 0 0 0
## sample_CTAGC_Div2 1 1 0 1 0 0 0 0
## sample_CTTGA_Div6 1 1 0 1 0 0 0 1
## sample_CTTGCTT_Div15 NA 1 0 1 0 0 0 NA
## sample_GTATT_Div10 1 1 0 1 0 1 0 0
## sample_GTATT_Div7 NA 1 0 1 0 0 0 0
## sample_TGACCA_Div5 1 1 0 1 0 0 0 1
## sample_TTAGGC_Div4 0 1 0 1 0 0 0 0
## [,910] [,911] [,912] [,913] [,914] [,915] [,916] [,917]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 NA
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 NA
## sample_ATGAAAC_Nel15 0 0 0 1 0 0 0 0
## sample_CGATGT_Nel4 0 1 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 1 0 0 NA
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 1
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 1 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 1 1 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 1 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA 0 0 0 NA 0
## sample_ACAAA_Sub1 0 NA NA 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 NA 0 0 0 0
## sample_CGATGT_Sub6 NA NA 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA 0 NA NA 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 NA NA 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 NA 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 NA 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 0 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 NA 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 1 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 1 0
## sample_AAAAGTT_Div12 0 0 NA 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 NA 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 NA 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 NA 0 0 0 0 0
## sample_CGATGT_Div3 1 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 NA 0 NA NA 0 1 0 0
## sample_GTATT_Div10 0 0 NA 0 0 0 0 0
## sample_GTATT_Div7 0 0 NA 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,918] [,919] [,920] [,921] [,922] [,923] [,924] [,925]
## sample_ACAAA_Nel3 1 1 0 0 0 0 0 0
## sample_ACAGTG_Nel5 1 1 0 0 0 0 0 0
## sample_AGCAT_Nel8 1 1 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 1 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 1 0 0 0 1 1
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 NA NA 1 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 1 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 1 1 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 0 0 1 1
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 1 1 0 0 0 0 1 1
## sample_CTGTA_Alt14 0 0 0 0 0 0 1 1
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 1 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 0 0 0 0
## sample_ACAAA_Sub1 0 0 0 1 0 NA NA NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 1 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 1 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 NA NA NA
## sample_CTTGCTT_Sub14 NA NA 0 1 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 1 0 0 0 0
## sample_GTATT_Sub12 NA NA 0 0 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 1 0 0 0 0
## sample_ACAGTG_Cau2 NA NA 0 1 0 0 0 0
## sample_ACAGTG_Cau3 NA NA 0 1 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 1 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 1 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Cau12 NA NA 0 1 0 NA NA NA
## sample_CTAGC_Cau5 0 0 0 1 0 0 0 0
## sample_CTGTA_Cau8 NA NA 0 1 0 NA NA NA
## sample_GGACCTA_Cau13 0 0 0 1 0 0 0 0
## sample_TCACC_Cau1 0 0 0 1 0 0 0 0
## sample_TCACC_Cau4 0 0 0 1 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 1 1 0 0 0
## sample_AAAAGTT_Div13 0 0 0 1 0 0 0 0
## sample_ACTAT_Div14 0 0 0 1 0 0 0 0
## sample_AGCAT_Div11 NA NA 0 1 0 0 0 0
## sample_AGCCC_Div9 0 0 0 1 0 0 0 0
## sample_ATCACG_Div1 0 0 0 1 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 1 0 NA NA NA
## sample_CGATGT_Div3 NA NA 0 1 0 0 0 0
## sample_CTAGC_Div2 0 0 0 1 0 0 0 0
## sample_CTTGA_Div6 0 0 0 1 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 1 0 NA NA NA
## sample_GTATT_Div10 NA NA 0 1 0 0 0 0
## sample_GTATT_Div7 NA NA 0 1 0 0 0 0
## sample_TGACCA_Div5 NA NA 0 1 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 1 0 0 0 0
## [,926] [,927] [,928] [,929] [,930] [,931] [,932] [,933]
## sample_ACAAA_Nel3 0 0 0 0 1 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 1 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 1 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 0 0 0 1 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 1 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 0 0 1 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 1 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 1 0 0 0 0
## sample_ACAGTG_Alt3 1 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 1 0 0 1 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 1 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA 0 0 0 NA NA NA NA
## sample_ACAAA_Sub1 NA 0 0 0 NA NA NA NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 1 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 1 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA 0 0 0 NA NA NA NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 1 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA 0 NA 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 NA 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 1 1 0
## sample_ACTAT_Cau9 0 0 1 0 0 1 1 0
## sample_AGCCC_Cau7 0 0 1 0 NA NA NA NA
## sample_ATGAAAC_Cau12 NA 0 1 0 0 1 1 0
## sample_CTAGC_Cau5 0 0 0 0 0 1 1 0
## sample_CTGTA_Cau8 NA 0 0 0 NA NA NA NA
## sample_GGACCTA_Cau13 0 0 1 0 NA NA NA NA
## sample_TCACC_Cau1 0 0 0 0 0 1 1 0
## sample_TCACC_Cau4 0 0 1 0 NA NA NA NA
## sample_TGACCA_Cau6 0 0 0 0 0 1 1 0
## sample_AAAAGTT_Div12 0 0 0 0 0 1 1 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 1 1 0
## sample_AGCAT_Div11 0 0 0 0 0 1 1 0
## sample_AGCCC_Div9 0 0 0 0 0 1 1 0
## sample_ATCACG_Div1 0 0 0 0 NA NA NA NA
## sample_ATGAAAC_Div8 0 0 0 0 NA NA NA NA
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 NA NA NA NA
## sample_CTTGA_Div6 0 0 0 0 0 1 1 0
## sample_CTTGCTT_Div15 NA 0 1 0 0 1 1 0
## sample_GTATT_Div10 0 0 0 0 0 1 1 0
## sample_GTATT_Div7 0 0 0 0 0 1 1 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 1 1 0
## [,934] [,935] [,936] [,937] [,938] [,939] [,940] [,941]
## sample_ACAAA_Nel3 1 0 0 0 0 0 0 1
## sample_ACAGTG_Nel5 1 0 0 0 0 0 0 1
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 1
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 1 0 0 0 0 0 1 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 1
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 1 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 1
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 1 0 0 0 0 0 0 1
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 1 0 0 0 0 0 0 1
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 1
## sample_AGCCC_Alt13 1 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 1 0 0 0 0 1
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 1 0 0 0 0 0 0 1
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA 0 NA NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 NA NA NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 1
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 1
## sample_AGCCC_Sub11 0 0 0 0 0 NA NA NA
## sample_CGATGT_Sub6 0 0 0 NA NA 0 0 1
## sample_CTTGCTT_Sub14 0 0 0 0 0 NA 0 1
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 1
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 1
## sample_GTATT_Sub12 NA NA NA NA NA 0 NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 1
## sample_ACAGTG_Cau2 0 0 0 0 0 1 NA NA
## sample_ACAGTG_Cau3 0 0 0 0 0 1 0 1
## sample_ACTAT_Cau11 0 0 0 0 0 1 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 1 0 1
## sample_AGCCC_Cau7 0 0 0 0 0 NA NA NA
## sample_ATGAAAC_Cau12 0 0 0 0 NA NA 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 1 0 0
## sample_CTGTA_Cau8 NA NA NA 0 NA 1 NA NA
## sample_GGACCTA_Cau13 0 0 0 0 0 1 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 1
## sample_TCACC_Cau4 0 0 0 0 0 1 NA NA
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 1
## sample_AAAAGTT_Div12 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 1 0 0
## sample_ACTAT_Div14 0 0 0 0 0 1 0 0
## sample_AGCAT_Div11 0 0 0 0 0 1 0 0
## sample_AGCCC_Div9 0 0 0 0 1 1 0 0
## sample_ATCACG_Div1 0 0 0 0 0 1 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 1 0 1
## sample_CGATGT_Div3 0 1 0 0 0 1 0 0
## sample_CTAGC_Div2 0 0 0 1 0 1 0 1
## sample_CTTGA_Div6 0 0 0 0 0 1 0 1
## sample_CTTGCTT_Div15 0 0 0 0 0 1 0 0
## sample_GTATT_Div10 0 0 0 NA 0 1 0 0
## sample_GTATT_Div7 0 0 0 0 0 1 0 1
## sample_TGACCA_Div5 0 0 0 0 0 1 0 1
## sample_TTAGGC_Div4 0 0 0 0 0 1 0 0
## [,942] [,943] [,944] [,945] [,946] [,947] [,948] [,949]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 1 0 0 0 0 1
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 1 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 1
## sample_CTAGC_Nel7 0 0 0 0 1 1 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 1
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 1 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 1 0 0 0
## sample_AGCCC_Alt13 0 1 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 1 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 1 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA 0 0 0 0
## sample_ACAAA_Sub1 NA 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 NA 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 NA NA NA 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA NA NA 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 1
## sample_ACAGTG_Cau2 NA NA NA NA 0 0 0 1
## sample_ACAGTG_Cau3 0 NA NA NA 0 0 0 1
## sample_ACTAT_Cau11 1 0 0 0 0 0 0 1
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 1
## sample_AGCCC_Cau7 NA 0 0 0 0 0 0 1
## sample_ATGAAAC_Cau12 0 NA NA NA 0 0 0 1
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 1
## sample_CTGTA_Cau8 NA 0 0 0 0 0 0 1
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0 1
## sample_TCACC_Cau1 0 0 0 0 0 0 0 1
## sample_TCACC_Cau4 NA NA NA NA 0 0 0 1
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 1
## sample_AAAAGTT_Div12 0 NA NA NA 0 0 0 1
## sample_AAAAGTT_Div13 0 NA NA NA 0 0 0 1
## sample_ACTAT_Div14 0 0 0 0 0 0 0 1
## sample_AGCAT_Div11 0 NA NA NA 0 0 0 1
## sample_AGCCC_Div9 1 0 0 0 0 0 0 1
## sample_ATCACG_Div1 1 0 0 0 0 0 0 1
## sample_ATGAAAC_Div8 1 0 0 0 0 0 0 1
## sample_CGATGT_Div3 0 0 0 0 0 0 1 1
## sample_CTAGC_Div2 0 0 0 0 0 0 0 1
## sample_CTTGA_Div6 1 0 0 0 0 0 0 1
## sample_CTTGCTT_Div15 0 NA NA NA 0 0 0 1
## sample_GTATT_Div10 1 0 0 0 0 0 0 1
## sample_GTATT_Div7 0 0 0 0 0 0 0 1
## sample_TGACCA_Div5 0 0 0 0 0 0 0 1
## sample_TTAGGC_Div4 1 0 0 0 0 0 0 1
## [,950] [,951] [,952] [,953] [,954] [,955] [,956] [,957]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 1 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 1 0 0 0 0 0 NA 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 1
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 1 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 1 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 1 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 NA NA NA NA 0 0 NA
## sample_ACAAA_Sub1 0 NA 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 NA 0 0 0 NA 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 NA 0 NA
## sample_CTTGCTT_Sub14 0 0 0 NA NA NA 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA 0 0 0 NA 0 NA
## sample_TGACCA_Sub2 1 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 1 0 0 NA NA 0 1 0
## sample_ACAGTG_Cau3 1 0 0 1 1 0 1 NA
## sample_ACTAT_Cau11 1 0 0 1 1 0 1 0
## sample_ACTAT_Cau9 1 0 0 1 1 0 1 0
## sample_AGCCC_Cau7 1 NA 0 1 1 0 1 NA
## sample_ATGAAAC_Cau12 1 NA 0 1 1 0 NA NA
## sample_CTAGC_Cau5 1 0 1 1 0 0 1 0
## sample_CTGTA_Cau8 1 NA 0 1 1 NA NA NA
## sample_GGACCTA_Cau13 1 NA 0 1 1 0 1 0
## sample_TCACC_Cau1 1 0 0 1 0 0 1 0
## sample_TCACC_Cau4 1 0 0 1 0 1 1 0
## sample_TGACCA_Cau6 1 0 0 1 1 0 1 0
## sample_AAAAGTT_Div12 1 0 0 1 1 0 1 0
## sample_AAAAGTT_Div13 1 0 0 1 1 0 1 0
## sample_ACTAT_Div14 1 0 0 1 1 0 1 0
## sample_AGCAT_Div11 1 0 0 NA NA 0 1 0
## sample_AGCCC_Div9 1 0 0 1 0 0 1 0
## sample_ATCACG_Div1 1 0 0 1 1 0 1 0
## sample_ATGAAAC_Div8 1 0 0 NA NA 0 1 0
## sample_CGATGT_Div3 1 0 0 1 1 0 1 0
## sample_CTAGC_Div2 1 0 1 1 0 0 1 0
## sample_CTTGA_Div6 1 0 0 1 1 0 1 0
## sample_CTTGCTT_Div15 1 0 0 NA NA 0 1 0
## sample_GTATT_Div10 1 0 0 1 1 0 1 0
## sample_GTATT_Div7 1 0 0 NA NA 0 1 NA
## sample_TGACCA_Div5 1 0 0 1 1 0 1 0
## sample_TTAGGC_Div4 1 0 0 1 1 0 1 0
## [,958] [,959] [,960] [,961] [,962] [,963] [,964] [,965]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 1 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 1 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 1 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 1 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 1 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 1 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 1 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 1 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 1 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 1 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 1 0 0 0 1 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 1 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA 0 NA NA NA 0 0 0
## sample_ACAAA_Sub1 0 0 NA NA NA 0 0 0
## sample_ACTAT_Sub7 0 0 1 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 1 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 NA 0 NA NA NA 0 NA 0
## sample_CTTGCTT_Sub14 0 NA NA NA NA 0 NA 0
## sample_GAATTCA_Sub9 0 0 1 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 1 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 0 0 0 NA NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 1 NA NA NA NA NA 1
## sample_ACAGTG_Cau3 NA 1 0 1 0 0 0 1
## sample_ACTAT_Cau11 0 1 0 1 0 0 0 1
## sample_ACTAT_Cau9 0 1 0 1 0 0 0 1
## sample_AGCCC_Cau7 NA 1 0 1 0 0 0 1
## sample_ATGAAAC_Cau12 NA 1 0 1 0 0 NA 1
## sample_CTAGC_Cau5 0 1 0 1 0 0 0 1
## sample_CTGTA_Cau8 NA 1 0 1 0 NA 0 1
## sample_GGACCTA_Cau13 0 1 0 1 0 0 0 1
## sample_TCACC_Cau1 0 1 0 1 0 0 0 1
## sample_TCACC_Cau4 0 1 0 1 0 0 NA 1
## sample_TGACCA_Cau6 0 1 0 0 1 0 0 1
## sample_AAAAGTT_Div12 1 1 0 0 1 0 0 1
## sample_AAAAGTT_Div13 0 1 0 1 0 0 0 1
## sample_ACTAT_Div14 0 1 0 1 0 0 0 1
## sample_AGCAT_Div11 1 1 0 1 0 0 0 1
## sample_AGCCC_Div9 0 1 0 1 0 0 0 1
## sample_ATCACG_Div1 0 1 0 1 0 0 0 1
## sample_ATGAAAC_Div8 0 1 0 1 0 0 0 1
## sample_CGATGT_Div3 0 1 0 1 0 0 0 1
## sample_CTAGC_Div2 0 0 0 1 0 0 0 1
## sample_CTTGA_Div6 0 1 0 1 0 0 0 1
## sample_CTTGCTT_Div15 0 1 0 1 0 1 0 1
## sample_GTATT_Div10 0 1 0 1 0 0 0 1
## sample_GTATT_Div7 NA 0 0 1 0 0 0 1
## sample_TGACCA_Div5 0 1 0 1 0 0 0 1
## sample_TTAGGC_Div4 0 1 0 1 0 0 0 1
## [,966] [,967] [,968] [,969] [,970] [,971] [,972] [,973]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 1 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 1 0 0 0 1 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 1 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 1 0 1 0
## sample_GGACCTA_Nel11 0 0 1 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 1 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 1 1 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 1 0
## sample_ACAAA_Alt11 0 0 0 0 1 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 1 0 1 0
## sample_AGCCC_Alt13 0 0 0 0 1 0 1 0
## sample_ATCACG_Alt5 0 1 0 0 1 0 1 0
## sample_ATCACG_Alt7 0 0 0 0 1 0 1 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 1 0
## sample_CTGTA_Alt14 1 0 0 0 0 0 1 0
## sample_CTTGA_Alt10 0 0 0 0 1 0 1 0
## sample_GAATTCA_Alt15 0 0 0 0 1 0 0 0
## sample_GCCAAT_Alt4 0 1 0 0 1 0 1 0
## sample_GCCAAT_Alt9 0 0 1 0 0 0 1 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 1 0
## sample_TTAGGC_Alt6 0 0 0 0 1 0 0 0
## sample_TTAGGC_Alt8 0 1 0 0 1 0 0 0
## sample_AAAAGTT_Sub15 0 NA NA NA 0 NA NA 0
## sample_ACAAA_Sub1 0 NA 0 NA 1 0 NA 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 NA NA 0 0 0
## sample_CTTGCTT_Sub14 0 NA NA 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 1 0 0 0
## sample_GTATT_Sub12 0 NA NA NA NA 0 NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 NA 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 NA 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0 1
## sample_ATGAAAC_Cau12 0 NA 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 NA NA NA 0 0 NA 0
## sample_GGACCTA_Cau13 0 0 0 NA 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 1 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0 1
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 NA 0 0 0 0 1
## sample_ACTAT_Div14 0 0 NA 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0 1
## sample_AGCCC_Div9 0 0 0 0 0 0 0 1
## sample_ATCACG_Div1 0 0 NA 0 0 0 0 1
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0 1
## sample_CTTGA_Div6 0 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 NA 0 0 0 0 0
## sample_GTATT_Div10 0 0 NA 0 0 0 0 0
## sample_GTATT_Div7 0 0 NA 0 0 0 0 0
## sample_TGACCA_Div5 0 0 NA 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0 0
## [,974] [,975] [,976] [,977] [,978] [,979] [,980] [,981]
## sample_ACAAA_Nel3 0 0 1 0 0 1 1 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 1 0 1 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 1 0 0
## sample_ATGAAAC_Nel15 0 0 0 1 0 1 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 1 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 1 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 1 0 0 1 0
## sample_CTTGA_Nel2 0 0 0 1 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 1 0
## sample_GTATT_Nel14 0 0 0 0 0 0 1 0
## sample_TCACC_Nel6 0 0 0 0 0 1 1 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 1 0
## sample_ACAAA_Alt11 0 0 0 1 0 0 1 0
## sample_ACAGTG_Alt3 0 0 0 1 0 0 1 0
## sample_AGCCC_Alt13 0 0 0 0 0 1 1 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 1 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 1 0
## sample_CGATGT_Alt1 0 0 0 1 0 0 1 0
## sample_CTGTA_Alt14 0 0 0 1 0 1 1 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 1 0
## sample_GAATTCA_Alt15 0 0 0 0 0 1 1 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 1 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 1 1 0
## sample_TTAGGC_Alt6 0 0 0 1 0 1 1 0
## sample_TTAGGC_Alt8 0 0 0 1 0 0 1 0
## sample_AAAAGTT_Sub15 0 NA 0 NA NA NA 0 0
## sample_ACAAA_Sub1 0 0 0 NA 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 1 0
## sample_AGCCC_Sub11 0 0 NA 0 0 0 1 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 1 0
## sample_CTTGCTT_Sub14 0 NA 0 0 0 0 1 0
## sample_GAATTCA_Sub9 0 0 0 0 1 0 1 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0 0
## sample_GTATT_Sub12 1 NA NA NA 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 1 0
## sample_ACAGTG_Cau2 0 1 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 1 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 1 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 1 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 1 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 1 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 1 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 NA 0 0 0 0 0 1
## sample_GGACCTA_Cau13 0 1 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 1 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 1 0 0 0 0 0 0
## sample_ACTAT_Div14 0 1 0 0 0 0 0 0
## sample_AGCAT_Div11 0 1 0 0 0 0 0 0
## sample_AGCCC_Div9 0 1 0 0 0 0 0 0
## sample_ATCACG_Div1 0 1 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 1 0 0 0 0 0 0
## sample_CGATGT_Div3 0 1 0 0 0 0 0 0
## sample_CTAGC_Div2 0 1 0 0 0 0 0 0
## sample_CTTGA_Div6 0 1 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 1 0 0 0 0 0 0
## sample_GTATT_Div10 0 1 0 0 0 0 0 0
## sample_GTATT_Div7 0 1 0 0 0 0 0 0
## sample_TGACCA_Div5 0 1 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 1 0 0 0 0 0 0
## [,982] [,983] [,984] [,985] [,986] [,987] [,988] [,989]
## sample_ACAAA_Nel3 0 0 0 1 0 1 0 0
## sample_ACAGTG_Nel5 0 0 0 1 0 1 0 0
## sample_AGCAT_Nel8 0 0 0 1 0 1 0 0
## sample_ATGAAAC_Nel10 0 0 0 1 0 1 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 1 0 0
## sample_CGATGT_Nel4 0 0 0 1 0 1 0 0
## sample_CTAGC_Nel7 1 0 0 0 0 1 0 0
## sample_CTGTA_Nel12 1 1 0 1 0 0 0 1
## sample_CTGTA_Nel9 0 0 0 0 0 1 0 0
## sample_CTTGA_Nel2 0 0 0 1 0 1 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 1 0 0
## sample_GGACCTA_Nel13 0 0 0 1 0 1 0 0
## sample_GTATT_Nel14 0 0 0 1 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 1 0 0
## sample_TGACCA_Nel1 0 0 0 1 0 1 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 1 0 0
## sample_ACAAA_Alt11 0 0 0 1 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 1 0 1 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 1 0 0
## sample_ATCACG_Alt5 0 0 0 0 1 1 0 0
## sample_ATCACG_Alt7 0 0 0 1 0 1 0 0
## sample_CGATGT_Alt1 0 0 0 1 0 1 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 1 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 1 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 1 0 0
## sample_GCCAAT_Alt9 0 0 0 1 0 1 0 0
## sample_TTAGGC_Alt2 0 0 0 1 0 1 0 0
## sample_TTAGGC_Alt6 0 0 0 1 0 1 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 1 0 0
## sample_AAAAGTT_Sub15 0 0 NA NA NA NA NA 0
## sample_ACAAA_Sub1 0 0 0 1 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 1 0 1 0 0
## sample_AGCAT_Sub13 0 0 0 1 0 0 0 0
## sample_AGCCC_Sub11 0 0 NA 0 0 1 0 0
## sample_CGATGT_Sub6 0 0 0 1 0 1 NA 0
## sample_CTTGCTT_Sub14 0 0 NA NA NA NA 0 0
## sample_GAATTCA_Sub9 0 0 0 1 0 1 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 1 0 0
## sample_GTATT_Sub12 0 0 0 NA NA 1 NA 0
## sample_TGACCA_Sub2 0 0 NA 1 0 NA 0 0
## sample_ACAGTG_Cau2 0 0 1 0 0 NA 0 NA
## sample_ACAGTG_Cau3 0 0 1 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 1 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 1 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 1 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 1 0 0 NA 0 0
## sample_CTAGC_Cau5 0 0 1 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 1 0 0 NA 0 0
## sample_GGACCTA_Cau13 0 0 1 0 0 0 0 NA
## sample_TCACC_Cau1 0 0 1 0 0 0 0 NA
## sample_TCACC_Cau4 0 0 1 0 0 0 0 NA
## sample_TGACCA_Cau6 0 0 1 0 0 0 0 NA
## sample_AAAAGTT_Div12 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 1 0 0 0 0 NA
## sample_ACTAT_Div14 0 0 1 0 0 0 0 NA
## sample_AGCAT_Div11 0 0 1 0 0 0 0 NA
## sample_AGCCC_Div9 0 0 1 0 0 0 0 0
## sample_ATCACG_Div1 0 0 1 0 0 0 0 NA
## sample_ATGAAAC_Div8 0 0 1 0 0 0 0 0
## sample_CGATGT_Div3 0 0 1 0 0 0 1 0
## sample_CTAGC_Div2 0 0 1 0 0 0 0 NA
## sample_CTTGA_Div6 0 0 1 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 1 0 0 NA 0 0
## sample_GTATT_Div10 0 0 1 0 0 0 0 0
## sample_GTATT_Div7 0 0 1 0 0 0 0 NA
## sample_TGACCA_Div5 0 0 1 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 1 0 0 0 0 NA
## [,990] [,991] [,992] [,993] [,994] [,995] [,996] [,997]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 1 1 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 1 1 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 1 1 0 1 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 1 1 0 0 0 0 0
## sample_CTGTA_Nel12 0 1 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 1 0 0 1 0 0 0
## sample_CTTGA_Nel2 0 1 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 1 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 1 0 0 0 0 0 0
## sample_TCACC_Nel6 0 1 1 0 0 0 0 0
## sample_TGACCA_Nel1 0 1 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 1 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 1 1 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 1 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt2 1 0 0 0 1 0 0 0
## sample_TTAGGC_Alt6 0 1 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 1 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 NA 0 NA NA NA
## sample_ACAAA_Sub1 0 0 NA 0 0 0 0 0
## sample_ACTAT_Sub7 0 1 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 1 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 1 0 NA 0 0
## sample_CTTGCTT_Sub14 0 NA 0 0 0 NA 0 0
## sample_GAATTCA_Sub9 0 1 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 1 0 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 0 0 0 NA 0 NA
## sample_TGACCA_Sub2 0 NA 1 0 0 0 0 0
## sample_ACAGTG_Cau2 0 NA 0 1 0 NA 1 0
## sample_ACAGTG_Cau3 0 0 0 1 0 1 1 0
## sample_ACTAT_Cau11 0 0 0 1 0 1 1 1
## sample_ACTAT_Cau9 0 0 0 1 0 1 1 0
## sample_AGCCC_Cau7 0 0 0 1 0 1 1 0
## sample_ATGAAAC_Cau12 0 0 0 1 0 NA 1 0
## sample_CTAGC_Cau5 0 0 0 1 0 1 1 NA
## sample_CTGTA_Cau8 0 0 0 1 0 NA 1 NA
## sample_GGACCTA_Cau13 0 0 0 1 0 1 1 0
## sample_TCACC_Cau1 0 0 0 0 0 1 1 0
## sample_TCACC_Cau4 0 0 0 1 0 1 1 0
## sample_TGACCA_Cau6 0 0 0 1 0 1 1 0
## sample_AAAAGTT_Div12 0 0 0 1 0 1 1 0
## sample_AAAAGTT_Div13 0 0 0 1 0 1 1 0
## sample_ACTAT_Div14 0 0 0 1 0 1 1 0
## sample_AGCAT_Div11 NA 0 0 1 0 1 1 0
## sample_AGCCC_Div9 0 0 0 1 0 1 1 0
## sample_ATCACG_Div1 NA 0 0 1 0 1 1 0
## sample_ATGAAAC_Div8 NA 0 0 1 0 1 1 0
## sample_CGATGT_Div3 0 0 0 1 0 1 1 0
## sample_CTAGC_Div2 0 0 0 1 0 1 1 0
## sample_CTTGA_Div6 0 0 0 1 0 1 1 0
## sample_CTTGCTT_Div15 0 0 0 1 0 1 1 0
## sample_GTATT_Div10 0 0 0 1 0 1 1 0
## sample_GTATT_Div7 0 0 0 1 0 1 1 0
## sample_TGACCA_Div5 0 0 0 1 0 1 1 0
## sample_TTAGGC_Div4 0 0 0 1 0 1 1 0
## [,998] [,999] [,1000] [,1001] [,1002] [,1003] [,1004]
## sample_ACAAA_Nel3 0 0 0 0 1 0 0
## sample_ACAGTG_Nel5 0 0 1 0 0 0 0
## sample_AGCAT_Nel8 0 0 1 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 1 0 0 NA NA
## sample_ATGAAAC_Nel15 0 0 0 1 0 0 0
## sample_CGATGT_Nel4 0 0 1 1 0 NA NA
## sample_CTAGC_Nel7 0 0 0 0 0 1 1
## sample_CTGTA_Nel12 0 0 1 0 1 0 0
## sample_CTGTA_Nel9 0 0 1 0 0 0 0
## sample_CTTGA_Nel2 0 0 1 0 0 0 0
## sample_GGACCTA_Nel11 0 0 1 0 0 0 0
## sample_GGACCTA_Nel13 0 0 1 0 0 NA NA
## sample_GTATT_Nel14 0 0 1 0 0 0 0
## sample_TCACC_Nel6 0 0 1 0 0 0 0
## sample_TGACCA_Nel1 0 0 1 0 0 NA NA
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 1 0 0
## sample_ACAGTG_Alt3 0 0 1 0 0 0 0
## sample_AGCCC_Alt13 0 0 1 1 0 0 0
## sample_ATCACG_Alt5 0 0 1 1 0 0 0
## sample_ATCACG_Alt7 0 0 1 0 0 0 0
## sample_CGATGT_Alt1 0 0 1 0 0 0 0
## sample_CTGTA_Alt14 0 0 1 1 0 0 0
## sample_CTTGA_Alt10 0 0 1 0 0 0 0
## sample_GAATTCA_Alt15 0 0 1 0 0 0 0
## sample_GCCAAT_Alt4 0 0 1 0 0 0 0
## sample_GCCAAT_Alt9 0 0 1 0 0 0 0
## sample_TTAGGC_Alt2 0 0 1 0 0 0 0
## sample_TTAGGC_Alt6 0 0 1 0 0 NA NA
## sample_TTAGGC_Alt8 0 0 1 0 1 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA NA NA
## sample_ACAAA_Sub1 0 NA 1 NA NA 0 0
## sample_ACTAT_Sub7 0 0 1 0 0 0 0
## sample_AGCAT_Sub13 0 0 1 1 0 0 0
## sample_AGCCC_Sub11 0 0 1 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 NA NA
## sample_CTTGCTT_Sub14 0 0 1 0 0 NA NA
## sample_GAATTCA_Sub9 0 0 1 0 0 0 0
## sample_GGACCTA_Sub10 0 0 1 0 0 0 0
## sample_GTATT_Sub12 NA 0 NA 0 0 NA NA
## sample_TGACCA_Sub2 0 0 NA 0 0 0 0
## sample_ACAGTG_Cau2 0 NA NA 0 1 0 0
## sample_ACAGTG_Cau3 1 1 0 0 1 0 0
## sample_ACTAT_Cau11 0 1 0 0 1 0 0
## sample_ACTAT_Cau9 0 1 1 0 1 0 0
## sample_AGCCC_Cau7 0 1 0 0 1 0 0
## sample_ATGAAAC_Cau12 0 NA 1 0 1 0 0
## sample_CTAGC_Cau5 NA 1 1 0 1 0 0
## sample_CTGTA_Cau8 NA NA 0 NA NA 0 0
## sample_GGACCTA_Cau13 0 1 0 0 1 0 0
## sample_TCACC_Cau1 1 0 1 0 1 0 0
## sample_TCACC_Cau4 0 1 0 0 1 0 0
## sample_TGACCA_Cau6 0 1 0 0 1 0 0
## sample_AAAAGTT_Div12 0 1 1 0 1 0 0
## sample_AAAAGTT_Div13 0 1 0 0 1 0 0
## sample_ACTAT_Div14 1 1 1 0 1 0 0
## sample_AGCAT_Div11 0 1 1 0 1 0 0
## sample_AGCCC_Div9 0 1 0 0 1 0 0
## sample_ATCACG_Div1 0 1 1 0 1 0 0
## sample_ATGAAAC_Div8 0 1 1 0 1 0 0
## sample_CGATGT_Div3 1 1 1 0 1 0 0
## sample_CTAGC_Div2 1 1 0 0 1 0 0
## sample_CTTGA_Div6 1 1 0 0 1 0 0
## sample_CTTGCTT_Div15 0 NA 0 0 1 0 0
## sample_GTATT_Div10 0 1 0 0 1 0 0
## sample_GTATT_Div7 0 1 0 0 1 0 0
## sample_TGACCA_Div5 1 1 0 0 1 0 0
## sample_TTAGGC_Div4 0 1 0 0 1 0 0
## [,1005] [,1006] [,1007] [,1008] [,1009] [,1010] [,1011]
## sample_ACAAA_Nel3 0 0 0 1 0 0 0
## sample_ACAGTG_Nel5 0 0 1 1 0 0 0
## sample_AGCAT_Nel8 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel15 0 0 1 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 1 0 1 0
## sample_CTAGC_Nel7 0 0 1 1 0 0 0
## sample_CTGTA_Nel12 0 0 0 1 0 0 0
## sample_CTGTA_Nel9 0 0 0 1 0 0 0
## sample_CTTGA_Nel2 0 1 0 1 0 0 0
## sample_GGACCTA_Nel11 0 0 0 1 0 0 0
## sample_GGACCTA_Nel13 0 0 0 1 0 0 0
## sample_GTATT_Nel14 0 0 0 1 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 1
## sample_TGACCA_Nel1 0 0 0 1 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 0 1 1 0 0
## sample_ACAGTG_Alt3 0 0 0 1 0 0 0
## sample_AGCCC_Alt13 0 0 0 1 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 1 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 1 0 0
## sample_CTGTA_Alt14 0 0 0 1 0 0 0
## sample_CTTGA_Alt10 0 0 0 1 0 0 0
## sample_GAATTCA_Alt15 0 0 0 1 1 0 0
## sample_GCCAAT_Alt4 0 0 1 1 0 0 0
## sample_GCCAAT_Alt9 0 0 1 1 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 1 0 0 0
## sample_TTAGGC_Alt8 0 0 0 1 0 0 0
## sample_AAAAGTT_Sub15 NA 0 1 NA 0 0 1
## sample_ACAAA_Sub1 0 0 1 NA 0 NA NA
## sample_ACTAT_Sub7 0 0 1 1 0 0 1
## sample_AGCAT_Sub13 0 0 1 1 0 0 1
## sample_AGCCC_Sub11 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 1 1 0 NA NA
## sample_CTTGCTT_Sub14 NA 0 0 1 NA 0 0
## sample_GAATTCA_Sub9 0 0 0 1 0 0 0
## sample_GGACCTA_Sub10 0 0 1 1 0 0 0
## sample_GTATT_Sub12 0 0 1 1 NA NA NA
## sample_TGACCA_Sub2 0 0 1 1 0 NA NA
## sample_ACAGTG_Cau2 0 0 0 0 NA NA NA
## sample_ACAGTG_Cau3 NA 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 NA 0 0 0 0 0 0
## sample_CTAGC_Cau5 1 0 0 0 0 0 0
## sample_CTGTA_Cau8 NA 0 0 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 1 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 NA NA
## sample_AGCCC_Div9 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 0
## sample_GTATT_Div10 0 0 0 0 0 NA NA
## sample_GTATT_Div7 NA 0 0 0 0 NA NA
## sample_TGACCA_Div5 1 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1012] [,1013] [,1014] [,1015] [,1016] [,1017] [,1018]
## sample_ACAAA_Nel3 0 0 0 0 0 0 NA
## sample_ACAGTG_Nel5 0 0 0 0 0 0 1
## sample_AGCAT_Nel8 0 0 0 0 1 0 1
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 NA
## sample_CGATGT_Nel4 0 0 0 0 0 0 1
## sample_CTAGC_Nel7 0 0 0 0 0 0 NA
## sample_CTGTA_Nel12 0 0 0 0 0 0 1
## sample_CTGTA_Nel9 1 0 0 0 0 0 1
## sample_CTTGA_Nel2 0 0 0 0 0 1 1
## sample_GGACCTA_Nel11 0 0 0 0 0 1 1
## sample_GGACCTA_Nel13 0 0 0 0 0 0 1
## sample_GTATT_Nel14 NA 0 0 0 0 0 1
## sample_TCACC_Nel6 0 0 0 0 0 0 1
## sample_TGACCA_Nel1 0 0 0 0 0 0 1
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 1
## sample_ACAAA_Alt11 NA 0 0 0 0 0 1
## sample_ACAGTG_Alt3 0 0 0 0 0 0 1
## sample_AGCCC_Alt13 0 0 0 0 0 0 1
## sample_ATCACG_Alt5 0 0 0 0 0 0 1
## sample_ATCACG_Alt7 0 0 0 0 0 0 1
## sample_CGATGT_Alt1 0 0 0 0 0 0 1
## sample_CTGTA_Alt14 0 0 0 0 0 0 1
## sample_CTTGA_Alt10 NA 0 0 0 0 0 1
## sample_GAATTCA_Alt15 0 0 0 0 0 0 1
## sample_GCCAAT_Alt4 0 0 0 0 0 0 1
## sample_GCCAAT_Alt9 0 0 0 0 0 0 1
## sample_TTAGGC_Alt2 0 0 0 0 0 0 NA
## sample_TTAGGC_Alt6 0 0 0 0 0 0 1
## sample_TTAGGC_Alt8 0 0 0 0 0 0 1
## sample_AAAAGTT_Sub15 NA NA 1 0 NA NA 1
## sample_ACAAA_Sub1 1 NA 0 0 0 0 1
## sample_ACTAT_Sub7 0 0 0 0 0 0 1
## sample_AGCAT_Sub13 0 0 0 0 0 0 1
## sample_AGCCC_Sub11 0 0 0 1 0 0 1
## sample_CGATGT_Sub6 NA NA 0 0 0 0 1
## sample_CTTGCTT_Sub14 NA NA 0 NA 0 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 1
## sample_GGACCTA_Sub10 0 0 0 0 0 0 1
## sample_GTATT_Sub12 NA NA 0 0 NA NA 1
## sample_TGACCA_Sub2 1 0 0 NA 0 0 1
## sample_ACAGTG_Cau2 NA 0 0 1 0 0 0
## sample_ACAGTG_Cau3 0 0 0 1 NA NA 0
## sample_ACTAT_Cau11 0 0 0 1 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 1 0 0 0
## sample_ATGAAAC_Cau12 NA 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 1 0 0 0
## sample_CTGTA_Cau8 NA NA 0 NA NA NA 0
## sample_GGACCTA_Cau13 NA 0 0 1 0 0 0
## sample_TCACC_Cau1 0 0 0 1 0 0 0
## sample_TCACC_Cau4 0 0 0 1 NA NA 0
## sample_TGACCA_Cau6 0 0 0 1 0 0 0
## sample_AAAAGTT_Div12 0 0 0 1 0 0 0
## sample_AAAAGTT_Div13 0 0 0 1 0 0 0
## sample_ACTAT_Div14 0 1 0 1 NA NA 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 1 0 0 0
## sample_ATCACG_Div1 0 0 0 1 0 0 0
## sample_ATGAAAC_Div8 0 0 0 1 0 0 0
## sample_CGATGT_Div3 0 0 0 1 0 0 0
## sample_CTAGC_Div2 0 0 0 1 0 0 0
## sample_CTTGA_Div6 0 0 0 1 0 0 0
## sample_CTTGCTT_Div15 0 0 0 1 0 0 0
## sample_GTATT_Div10 0 0 0 1 0 0 0
## sample_GTATT_Div7 0 0 0 1 NA NA 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 1 0 0 0
## [,1019] [,1020] [,1021] [,1022] [,1023] [,1024] [,1025]
## sample_ACAAA_Nel3 0 0 0 0 0 0 1
## sample_ACAGTG_Nel5 0 0 0 0 0 0 1
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 1
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 1
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 1
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 1 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 1 0 0 1
## sample_CTTGA_Alt10 0 0 0 0 0 0 1
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 1
## sample_GCCAAT_Alt9 0 0 0 0 0 0 1
## sample_TTAGGC_Alt2 0 0 0 1 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 1 1
## sample_AAAAGTT_Sub15 0 NA 0 0 0 NA 1
## sample_ACAAA_Sub1 0 NA 0 0 0 NA 1
## sample_ACTAT_Sub7 0 0 0 0 0 0 1
## sample_AGCAT_Sub13 0 0 0 0 0 0 1
## sample_AGCCC_Sub11 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 NA 0 0 0 0 1
## sample_CTTGCTT_Sub14 0 NA 0 0 0 NA 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 1
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 1 0 0 0 0 0
## sample_ACAGTG_Cau3 0 NA 0 0 0 0 0
## sample_ACTAT_Cau11 0 1 0 0 0 0 0
## sample_ACTAT_Cau9 0 1 0 0 0 0 0
## sample_AGCCC_Cau7 0 NA 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 1 0 0 0 NA 0
## sample_CTAGC_Cau5 0 1 0 0 0 0 0
## sample_CTGTA_Cau8 0 NA 0 0 0 NA 0
## sample_GGACCTA_Cau13 0 1 0 0 0 0 0
## sample_TCACC_Cau1 0 NA 0 0 0 0 0
## sample_TCACC_Cau4 0 1 0 0 0 0 0
## sample_TGACCA_Cau6 0 1 0 0 0 0 0
## sample_AAAAGTT_Div12 0 1 1 0 0 0 0
## sample_AAAAGTT_Div13 0 1 0 0 0 0 0
## sample_ACTAT_Div14 0 1 0 0 0 0 0
## sample_AGCAT_Div11 0 1 0 0 1 0 0
## sample_AGCCC_Div9 0 NA 0 0 0 0 0
## sample_ATCACG_Div1 0 1 0 0 0 0 0
## sample_ATGAAAC_Div8 0 1 0 0 0 0 0
## sample_CGATGT_Div3 0 1 0 0 0 0 0
## sample_CTAGC_Div2 0 1 0 0 0 0 0
## sample_CTTGA_Div6 0 1 0 0 0 0 0
## sample_CTTGCTT_Div15 0 1 0 0 0 0 0
## sample_GTATT_Div10 0 1 0 0 0 0 0
## sample_GTATT_Div7 0 1 0 0 0 0 0
## sample_TGACCA_Div5 0 1 0 0 0 0 0
## sample_TTAGGC_Div4 0 1 0 0 0 0 0
## [,1026] [,1027] [,1028] [,1029] [,1030] [,1031] [,1032]
## sample_ACAAA_Nel3 1 0 0 0 0 0 0
## sample_ACAGTG_Nel5 1 0 0 1 0 0 0
## sample_AGCAT_Nel8 1 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 1 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 0 0 0 0 0 0
## sample_CGATGT_Nel4 1 0 0 0 0 0 0
## sample_CTAGC_Nel7 1 0 0 1 0 0 0
## sample_CTGTA_Nel12 1 0 0 0 0 0 0
## sample_CTGTA_Nel9 1 0 0 0 0 0 0
## sample_CTTGA_Nel2 1 0 0 1 0 0 0
## sample_GGACCTA_Nel11 1 0 0 1 0 0 0
## sample_GGACCTA_Nel13 1 0 0 0 0 0 0
## sample_GTATT_Nel14 1 0 0 0 0 0 0
## sample_TCACC_Nel6 1 0 0 0 0 0 0
## sample_TGACCA_Nel1 1 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 1 0 0 0 0 0 0
## sample_ACAAA_Alt11 1 0 0 1 0 0 0
## sample_ACAGTG_Alt3 1 0 0 0 0 0 0
## sample_AGCCC_Alt13 1 0 0 1 0 0 NA
## sample_ATCACG_Alt5 1 0 0 0 0 0 0
## sample_ATCACG_Alt7 1 0 0 1 0 0 0
## sample_CGATGT_Alt1 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 1 0 0 0 0 0 0
## sample_CTTGA_Alt10 1 0 0 0 0 0 0
## sample_GAATTCA_Alt15 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 1 0 0 1 0 0 0
## sample_GCCAAT_Alt9 1 0 0 1 0 0 0
## sample_TTAGGC_Alt2 0 0 0 1 0 0 0
## sample_TTAGGC_Alt6 1 0 0 0 0 0 0
## sample_TTAGGC_Alt8 1 0 1 0 0 0 0
## sample_AAAAGTT_Sub15 1 NA 0 1 0 0 NA
## sample_ACAAA_Sub1 NA NA 0 1 0 0 0
## sample_ACTAT_Sub7 1 0 0 0 0 0 0
## sample_AGCAT_Sub13 1 0 0 0 0 0 0
## sample_AGCCC_Sub11 1 NA 0 1 0 0 0
## sample_CGATGT_Sub6 1 0 NA NA 0 1 0
## sample_CTTGCTT_Sub14 NA 0 NA NA 0 0 0
## sample_GAATTCA_Sub9 1 0 0 1 0 0 0
## sample_GGACCTA_Sub10 1 0 0 1 0 0 1
## sample_GTATT_Sub12 NA NA 0 1 0 0 0
## sample_TGACCA_Sub2 NA 0 0 1 0 0 0
## sample_ACAGTG_Cau2 NA 0 0 0 1 1 0
## sample_ACAGTG_Cau3 0 0 0 0 0 1 0
## sample_ACTAT_Cau11 0 0 0 0 0 1 0
## sample_ACTAT_Cau9 0 0 0 0 0 1 0
## sample_AGCCC_Cau7 0 0 NA NA NA 1 0
## sample_ATGAAAC_Cau12 NA NA NA NA 1 1 0
## sample_CTAGC_Cau5 0 0 0 0 0 1 0
## sample_CTGTA_Cau8 0 0 NA NA 0 1 0
## sample_GGACCTA_Cau13 0 1 0 0 1 1 0
## sample_TCACC_Cau1 0 0 0 0 1 1 0
## sample_TCACC_Cau4 NA NA NA NA 0 1 0
## sample_TGACCA_Cau6 0 1 NA NA 0 1 0
## sample_AAAAGTT_Div12 0 0 0 0 0 1 0
## sample_AAAAGTT_Div13 0 0 NA NA 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 1 0
## sample_AGCAT_Div11 NA 0 0 0 0 1 0
## sample_AGCCC_Div9 0 0 NA NA 0 1 0
## sample_ATCACG_Div1 0 0 NA NA 1 0 0
## sample_ATGAAAC_Div8 0 0 0 0 1 1 0
## sample_CGATGT_Div3 0 0 0 0 0 1 0
## sample_CTAGC_Div2 0 0 0 0 0 1 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 NA NA NA 1 0
## sample_GTATT_Div10 NA 0 0 0 0 1 0
## sample_GTATT_Div7 0 1 NA NA 0 1 0
## sample_TGACCA_Div5 0 0 NA NA 0 1 0
## sample_TTAGGC_Div4 0 0 NA NA 0 1 0
## [,1033] [,1034] [,1035] [,1036] [,1037] [,1038] [,1039]
## sample_ACAAA_Nel3 0 0 1 0 0 0 0
## sample_ACAGTG_Nel5 0 0 1 0 0 0 1
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel15 0 0 1 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 1 0
## sample_GTATT_Nel14 0 0 1 0 1 0 1
## sample_TCACC_Nel6 0 0 1 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 1 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 1
## sample_ACAAA_Alt11 0 0 1 0 0 0 1
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 0 NA NA
## sample_ACAAA_Sub1 0 0 0 0 NA 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 1
## sample_AGCCC_Sub11 0 0 0 0 NA NA NA
## sample_CGATGT_Sub6 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 0 0 NA NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 NA NA
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 NA NA
## sample_CTAGC_Cau5 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 1 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 NA NA
## sample_TGACCA_Cau6 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 1 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 1 0 0 0
## sample_ATCACG_Div1 0 0 0 1 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 1 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 0
## sample_GTATT_Div10 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 1 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1040] [,1041] [,1042] [,1043] [,1044] [,1045] [,1046]
## sample_ACAAA_Nel3 0 0 1 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 1 1 1 0 0 0 0
## sample_ATGAAAC_Nel10 0 1 1 0 0 NA NA
## sample_ATGAAAC_Nel15 0 1 0 0 0 0 0
## sample_CGATGT_Nel4 0 1 1 0 0 0 0
## sample_CTAGC_Nel7 0 1 1 0 0 0 0
## sample_CTGTA_Nel12 0 1 1 0 0 0 0
## sample_CTGTA_Nel9 0 1 0 0 0 1 0
## sample_CTTGA_Nel2 0 1 1 0 0 0 0
## sample_GGACCTA_Nel11 0 1 0 0 0 NA NA
## sample_GGACCTA_Nel13 0 1 1 0 0 0 0
## sample_GTATT_Nel14 0 1 1 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 1 0 1 0 0 0 0
## sample_AAAAGTT_Alt12 0 1 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 0 NA NA
## sample_ACAGTG_Alt3 0 0 1 0 0 0 0
## sample_AGCCC_Alt13 0 1 1 0 0 NA NA
## sample_ATCACG_Alt5 0 1 1 0 0 0 0
## sample_ATCACG_Alt7 1 0 1 0 0 NA NA
## sample_CGATGT_Alt1 0 1 0 0 1 NA NA
## sample_CTGTA_Alt14 0 1 1 0 0 0 0
## sample_CTTGA_Alt10 0 1 0 0 0 0 0
## sample_GAATTCA_Alt15 0 1 1 0 0 0 0
## sample_GCCAAT_Alt4 0 1 1 0 0 0 0
## sample_GCCAAT_Alt9 0 1 1 0 1 NA NA
## sample_TTAGGC_Alt2 0 1 1 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 NA NA
## sample_TTAGGC_Alt8 0 1 1 0 1 1 1
## sample_AAAAGTT_Sub15 NA 0 0 NA NA 0 0
## sample_ACAAA_Sub1 0 NA 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 1 0 0 NA NA
## sample_AGCAT_Sub13 0 0 0 0 0 1 0
## sample_AGCCC_Sub11 NA NA 0 1 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 NA 0 NA 0 0 0
## sample_GAATTCA_Sub9 0 1 0 1 0 1 1
## sample_GGACCTA_Sub10 0 0 0 0 0 1 0
## sample_GTATT_Sub12 NA NA NA 0 0 0 0
## sample_TGACCA_Sub2 NA 0 1 1 0 0 0
## sample_ACAGTG_Cau2 0 NA 0 1 0 0 0
## sample_ACAGTG_Cau3 0 0 0 1 0 0 0
## sample_ACTAT_Cau11 0 0 0 1 0 0 0
## sample_ACTAT_Cau9 0 0 0 1 0 0 0
## sample_AGCCC_Cau7 0 0 0 NA 0 0 0
## sample_ATGAAAC_Cau12 NA 0 0 1 0 0 0
## sample_CTAGC_Cau5 0 0 0 1 0 0 0
## sample_CTGTA_Cau8 0 0 0 1 0 0 0
## sample_GGACCTA_Cau13 0 0 0 1 0 0 0
## sample_TCACC_Cau1 0 0 0 1 0 0 0
## sample_TCACC_Cau4 NA 0 0 1 0 0 0
## sample_TGACCA_Cau6 0 0 0 1 0 0 0
## sample_AAAAGTT_Div12 0 0 0 1 0 0 0
## sample_AAAAGTT_Div13 0 0 0 1 0 0 0
## sample_ACTAT_Div14 0 0 0 1 0 0 0
## sample_AGCAT_Div11 0 0 0 1 0 0 0
## sample_AGCCC_Div9 0 0 0 1 0 0 0
## sample_ATCACG_Div1 0 0 0 1 0 0 0
## sample_ATGAAAC_Div8 0 0 0 1 0 0 0
## sample_CGATGT_Div3 0 0 0 1 0 0 0
## sample_CTAGC_Div2 0 0 0 1 0 0 0
## sample_CTTGA_Div6 0 0 0 1 0 0 0
## sample_CTTGCTT_Div15 0 0 0 1 0 0 0
## sample_GTATT_Div10 0 0 0 1 0 0 0
## sample_GTATT_Div7 0 0 0 1 0 0 0
## sample_TGACCA_Div5 0 0 0 1 0 0 0
## sample_TTAGGC_Div4 0 0 0 1 0 0 0
## [,1047] [,1048] [,1049] [,1050] [,1051] [,1052] [,1053]
## sample_ACAAA_Nel3 1 1 1 1 0 0 0
## sample_ACAGTG_Nel5 1 1 1 1 0 0 0
## sample_AGCAT_Nel8 1 1 1 1 0 0 0
## sample_ATGAAAC_Nel10 NA NA NA NA NA 1 0
## sample_ATGAAAC_Nel15 1 1 1 1 0 0 0
## sample_CGATGT_Nel4 1 1 1 1 0 0 0
## sample_CTAGC_Nel7 1 1 1 1 0 0 0
## sample_CTGTA_Nel12 1 1 1 1 0 0 1
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 1 1 1 1 0 0 0
## sample_GGACCTA_Nel11 NA NA NA NA NA 0 0
## sample_GGACCTA_Nel13 1 1 1 1 0 1 0
## sample_GTATT_Nel14 1 1 1 1 0 0 0
## sample_TCACC_Nel6 1 1 1 1 0 0 0
## sample_TGACCA_Nel1 1 1 1 1 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0
## sample_ACAAA_Alt11 NA NA NA NA NA 0 0
## sample_ACAGTG_Alt3 1 1 1 1 0 0 0
## sample_AGCCC_Alt13 NA NA NA NA NA 0 0
## sample_ATCACG_Alt5 1 1 1 1 0 0 0
## sample_ATCACG_Alt7 NA NA NA NA NA 0 0
## sample_CGATGT_Alt1 NA NA NA NA NA 0 0
## sample_CTGTA_Alt14 1 1 1 1 0 0 0
## sample_CTTGA_Alt10 1 1 1 1 0 0 0
## sample_GAATTCA_Alt15 1 1 1 1 0 0 0
## sample_GCCAAT_Alt4 1 1 1 1 0 0 0
## sample_GCCAAT_Alt9 NA NA NA NA NA 0 0
## sample_TTAGGC_Alt2 1 1 1 1 0 0 0
## sample_TTAGGC_Alt6 NA NA NA NA NA 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 1 1 1 1 0 0 0
## sample_ACAAA_Sub1 1 1 1 1 0 0 0
## sample_ACTAT_Sub7 NA NA NA NA NA 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 1 1 1 1 0 0 0
## sample_CGATGT_Sub6 1 1 1 1 0 0 0
## sample_CTTGCTT_Sub14 1 1 1 1 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 1 1 1 1 0 0 0
## sample_TGACCA_Sub2 1 1 1 1 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 NA 0
## sample_ACAGTG_Cau3 1 1 1 1 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 1 1 1 1 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 0 0 0 0
## sample_GGACCTA_Cau13 1 1 1 1 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 0
## sample_GTATT_Div10 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1054] [,1055] [,1056] [,1057] [,1058] [,1059] [,1060]
## sample_ACAAA_Nel3 0 0 0 0 0 0 1
## sample_ACAGTG_Nel5 1 0 0 0 0 0 0
## sample_AGCAT_Nel8 1 0 1 0 NA 0 0
## sample_ATGAAAC_Nel10 1 0 0 0 0 NA 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 NA 0
## sample_CGATGT_Nel4 1 1 0 0 0 0 1
## sample_CTAGC_Nel7 1 0 0 0 0 0 0
## sample_CTGTA_Nel12 1 0 0 0 0 0 1
## sample_CTGTA_Nel9 1 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 1 0 0 0 0 NA 1
## sample_GGACCTA_Nel13 1 0 0 0 0 0 0
## sample_GTATT_Nel14 1 1 0 0 0 0 1
## sample_TCACC_Nel6 1 0 0 0 0 NA 0
## sample_TGACCA_Nel1 1 0 0 0 0 0 1
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 1
## sample_ACAAA_Alt11 1 0 0 0 0 0 0
## sample_ACAGTG_Alt3 1 0 0 0 0 0 1
## sample_AGCCC_Alt13 1 0 0 0 0 0 0
## sample_ATCACG_Alt5 1 0 0 0 0 0 0
## sample_ATCACG_Alt7 1 0 0 0 0 0 1
## sample_CGATGT_Alt1 0 0 0 0 0 NA 0
## sample_CTGTA_Alt14 0 0 0 0 0 NA 0
## sample_CTTGA_Alt10 0 0 0 0 NA 0 0
## sample_GAATTCA_Alt15 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 1 0 0 0 0 0 0
## sample_GCCAAT_Alt9 1 0 0 0 0 NA 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 1
## sample_TTAGGC_Alt6 1 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 0 NA NA 0
## sample_ACAAA_Sub1 NA NA 0 0 NA NA 0
## sample_ACTAT_Sub7 1 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 1 0 0 0 NA NA 0
## sample_CGATGT_Sub6 NA NA 0 0 0 0 0
## sample_CTTGCTT_Sub14 1 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA 0 0 NA 0 0
## sample_TGACCA_Sub2 1 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA NA 0 NA 1 0 0
## sample_ACAGTG_Cau3 NA NA 0 1 1 0 0
## sample_ACTAT_Cau11 0 0 0 1 1 0 0
## sample_ACTAT_Cau9 0 0 0 1 0 0 0
## sample_AGCCC_Cau7 0 0 0 1 NA 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 1 0 0
## sample_CTAGC_Cau5 0 0 0 1 1 0 0
## sample_CTGTA_Cau8 NA NA 0 1 NA 0 0
## sample_GGACCTA_Cau13 NA NA 0 0 1 0 0
## sample_TCACC_Cau1 0 0 0 1 1 0 0
## sample_TCACC_Cau4 NA NA 0 0 NA 0 0
## sample_TGACCA_Cau6 0 0 0 1 1 1 0
## sample_AAAAGTT_Div12 0 0 0 1 0 0 0
## sample_AAAAGTT_Div13 0 0 0 1 1 0 0
## sample_ACTAT_Div14 NA NA 0 1 1 0 0
## sample_AGCAT_Div11 0 0 0 1 NA 0 0
## sample_AGCCC_Div9 0 0 0 1 1 0 0
## sample_ATCACG_Div1 0 0 0 1 1 0 0
## sample_ATGAAAC_Div8 NA NA 0 1 1 0 0
## sample_CGATGT_Div3 0 0 0 1 0 0 0
## sample_CTAGC_Div2 0 0 0 1 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 1 NA 0 0
## sample_GTATT_Div10 0 0 0 1 0 0 0
## sample_GTATT_Div7 0 0 0 1 1 0 0
## sample_TGACCA_Div5 0 0 0 1 1 0 0
## sample_TTAGGC_Div4 NA NA 0 0 1 0 0
## [,1061] [,1062] [,1063] [,1064] [,1065] [,1066] [,1067]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 1 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 1 0 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 0 0 0 0 1
## sample_GGACCTA_Nel13 0 0 0 0 0 0 1
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 1 0
## sample_AAAAGTT_Alt12 1 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 1 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 1
## sample_ATCACG_Alt7 0 0 0 0 0 0 1
## sample_CGATGT_Alt1 0 0 0 0 0 0 1
## sample_CTGTA_Alt14 1 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 1 0 0 0 0 0 0
## sample_GCCAAT_Alt9 1 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 0 0 0 NA
## sample_ACAAA_Sub1 NA NA 0 0 0 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 1 0 0 0 0 0 1
## sample_AGCCC_Sub11 NA NA 0 1 1 0 0
## sample_CGATGT_Sub6 0 0 0 0 1 0 NA
## sample_CTTGCTT_Sub14 0 0 0 1 0 NA 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA 1 0 1 NA NA
## sample_TGACCA_Sub2 0 0 0 1 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 NA 0
## sample_ACAGTG_Cau3 0 0 0 0 0 1 0
## sample_ACTAT_Cau11 0 0 0 0 0 1 0
## sample_ACTAT_Cau9 0 0 NA NA NA 1 0
## sample_AGCCC_Cau7 0 0 NA NA NA NA 0
## sample_ATGAAAC_Cau12 NA NA 0 0 0 NA NA
## sample_CTAGC_Cau5 0 0 0 0 0 NA 0
## sample_CTGTA_Cau8 NA NA 0 0 0 1 NA
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 1 0
## sample_TCACC_Cau4 0 0 NA NA NA NA 0
## sample_TGACCA_Cau6 0 0 NA NA NA 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 1 0
## sample_ACTAT_Div14 0 0 NA NA NA 1 0
## sample_AGCAT_Div11 0 0 0 1 0 NA 0
## sample_AGCCC_Div9 0 0 NA NA NA 1 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 1 0
## sample_CGATGT_Div3 0 0 0 0 0 1 0
## sample_CTAGC_Div2 0 0 NA NA NA 0 0
## sample_CTTGA_Div6 0 0 0 0 0 1 0
## sample_CTTGCTT_Div15 0 0 0 0 0 NA 0
## sample_GTATT_Div10 0 0 0 1 0 1 0
## sample_GTATT_Div7 0 0 0 1 0 1 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 1 NA NA NA 1 0
## [,1068] [,1069] [,1070] [,1071] [,1072] [,1073] [,1074]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 NA NA NA NA NA NA 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 1 1 1 1 1 0
## sample_CGATGT_Nel4 NA NA NA NA NA NA 0
## sample_CTAGC_Nel7 NA NA NA NA NA NA 0
## sample_CTGTA_Nel12 NA NA NA NA NA NA NA
## sample_CTGTA_Nel9 NA NA NA NA NA NA 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 NA NA NA NA NA NA 0
## sample_GTATT_Nel14 1 1 1 1 1 1 0
## sample_TCACC_Nel6 NA NA NA NA NA NA 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 1 1 1 1 1 1 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 NA NA NA NA NA NA 0
## sample_ATCACG_Alt5 NA NA NA NA NA NA 0
## sample_ATCACG_Alt7 NA NA NA NA NA NA 1
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 NA NA NA NA NA NA 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 1 1 1 1 1 1 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 NA NA NA NA NA NA 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA NA 0
## sample_ACAAA_Sub1 1 1 1 1 1 1 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 NA NA NA NA NA NA 0
## sample_CGATGT_Sub6 1 1 1 1 1 1 0
## sample_CTTGCTT_Sub14 NA NA NA NA NA NA NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 1 1 1 1 1 1 0
## sample_GTATT_Sub12 1 1 1 1 1 1 NA
## sample_TGACCA_Sub2 NA NA NA NA NA NA 0
## sample_ACAGTG_Cau2 NA NA NA NA NA NA NA
## sample_ACAGTG_Cau3 1 1 1 1 1 1 0
## sample_ACTAT_Cau11 1 1 1 1 1 1 0
## sample_ACTAT_Cau9 1 1 1 1 1 1 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 NA NA NA NA NA NA NA
## sample_CTAGC_Cau5 NA NA NA NA NA NA 0
## sample_CTGTA_Cau8 1 1 1 1 1 1 0
## sample_GGACCTA_Cau13 1 1 1 1 1 1 0
## sample_TCACC_Cau1 1 1 1 1 1 1 0
## sample_TCACC_Cau4 NA NA NA NA NA NA 0
## sample_TGACCA_Cau6 NA NA NA NA NA NA 0
## sample_AAAAGTT_Div12 NA NA NA NA NA NA 0
## sample_AAAAGTT_Div13 NA NA NA NA NA NA 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0
## sample_AGCAT_Div11 NA NA NA NA NA NA NA
## sample_AGCCC_Div9 1 1 1 1 1 1 0
## sample_ATCACG_Div1 1 1 1 1 1 1 0
## sample_ATGAAAC_Div8 NA NA NA NA NA NA 0
## sample_CGATGT_Div3 NA NA NA NA NA NA 0
## sample_CTAGC_Div2 1 1 1 1 1 1 0
## sample_CTTGA_Div6 1 1 1 1 1 1 0
## sample_CTTGCTT_Div15 NA NA NA NA NA NA 0
## sample_GTATT_Div10 NA NA NA NA NA NA 0
## sample_GTATT_Div7 1 1 1 1 1 1 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1075] [,1076] [,1077] [,1078] [,1079] [,1080] [,1081]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 1 0 0 0 1 0
## sample_ATGAAAC_Nel10 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 NA 1 0 0 0 0 0
## sample_CTGTA_Nel9 0 1 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 1 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 1 0 0
## sample_GTATT_Nel14 1 0 0 0 0 0 1
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 1 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 1 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 1 0 0 1 0 0 0
## sample_CTGTA_Alt14 1 0 0 1 0 0 0
## sample_CTTGA_Alt10 0 1 0 0 0 0 0
## sample_GAATTCA_Alt15 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 1 0
## sample_GCCAAT_Alt9 1 NA 0 0 0 0 0
## sample_TTAGGC_Alt2 0 1 0 0 0 0 0
## sample_TTAGGC_Alt6 0 1 0 0 0 0 0
## sample_TTAGGC_Alt8 0 1 0 1 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 0 0 NA
## sample_ACAAA_Sub1 1 0 1 1 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 NA NA NA 0 0
## sample_CTTGCTT_Sub14 NA 0 0 0 0 0 0
## sample_GAATTCA_Sub9 1 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 0 0 0 0 0
## sample_TGACCA_Sub2 0 1 0 0 0 0 0
## sample_ACAGTG_Cau2 NA 0 0 1 0 NA 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 NA 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 NA NA NA NA 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 NA 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0
## sample_AGCAT_Div11 NA 0 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 NA 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 NA 0
## sample_GTATT_Div10 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 1 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1082] [,1083] [,1084] [,1085] [,1086] [,1087] [,1088]
## sample_ACAAA_Nel3 0 0 0 0 0 0 1
## sample_ACAGTG_Nel5 0 0 0 0 1 0 0
## sample_AGCAT_Nel8 0 1 1 1 0 0 0
## sample_ATGAAAC_Nel10 0 1 0 0 0 0 1
## sample_ATGAAAC_Nel15 0 1 0 0 0 0 1
## sample_CGATGT_Nel4 0 1 0 0 0 0 1
## sample_CTAGC_Nel7 0 1 0 1 0 0 0
## sample_CTGTA_Nel12 0 1 0 0 1 1 1
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 1 0 1
## sample_GGACCTA_Nel13 0 0 1 0 0 0 0
## sample_GTATT_Nel14 0 1 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 1 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 1 0 0 0 0 1
## sample_AGCCC_Alt13 0 0 0 0 0 0 1
## sample_ATCACG_Alt5 0 0 1 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 1 0 0 1
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 1 0 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 1 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA 0 NA 0 0 NA NA
## sample_ACAAA_Sub1 0 0 NA 0 0 0 0
## sample_ACTAT_Sub7 0 0 1 0 0 0 1
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 1 1 0 0 NA
## sample_CGATGT_Sub6 0 0 1 0 0 0 0
## sample_CTTGCTT_Sub14 0 NA 0 NA NA 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 1 NA NA 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 1 1 0 NA NA 0 0
## sample_ACAGTG_Cau3 1 1 0 0 0 0 0
## sample_ACTAT_Cau11 1 1 0 0 0 0 0
## sample_ACTAT_Cau9 1 1 0 0 0 0 0
## sample_AGCCC_Cau7 1 1 0 0 0 0 0
## sample_ATGAAAC_Cau12 1 1 0 0 0 0 NA
## sample_CTAGC_Cau5 1 1 0 0 0 0 0
## sample_CTGTA_Cau8 1 1 0 0 0 0 NA
## sample_GGACCTA_Cau13 1 1 0 0 0 0 0
## sample_TCACC_Cau1 1 1 0 0 0 0 0
## sample_TCACC_Cau4 1 1 0 0 0 0 0
## sample_TGACCA_Cau6 1 1 0 0 0 0 0
## sample_AAAAGTT_Div12 1 1 0 0 0 0 0
## sample_AAAAGTT_Div13 1 1 0 0 0 0 0
## sample_ACTAT_Div14 1 1 0 0 0 0 0
## sample_AGCAT_Div11 1 1 0 0 0 0 0
## sample_AGCCC_Div9 1 1 0 0 0 0 0
## sample_ATCACG_Div1 1 1 0 0 0 0 0
## sample_ATGAAAC_Div8 1 1 0 0 0 0 0
## sample_CGATGT_Div3 1 1 0 0 0 0 0
## sample_CTAGC_Div2 1 1 0 0 0 0 0
## sample_CTTGA_Div6 1 1 0 0 0 0 0
## sample_CTTGCTT_Div15 1 1 0 0 0 0 0
## sample_GTATT_Div10 1 1 0 0 0 0 0
## sample_GTATT_Div7 1 1 0 0 0 0 0
## sample_TGACCA_Div5 1 1 0 0 0 0 0
## sample_TTAGGC_Div4 1 1 0 0 0 0 0
## [,1089] [,1090] [,1091] [,1092] [,1093] [,1094] [,1095]
## sample_ACAAA_Nel3 0 0 0 0 1 0 0
## sample_ACAGTG_Nel5 1 0 0 0 1 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 1 0 1 0 0 0
## sample_CTAGC_Nel7 1 0 0 1 0 0 1
## sample_CTGTA_Nel12 0 1 0 1 0 0 0
## sample_CTGTA_Nel9 0 0 0 1 0 0 0
## sample_CTTGA_Nel2 0 0 0 1 0 0 0
## sample_GGACCTA_Nel11 0 0 0 1 0 0 0
## sample_GGACCTA_Nel13 0 1 0 0 0 0 1
## sample_GTATT_Nel14 0 1 0 0 1 0 0
## sample_TCACC_Nel6 0 0 0 1 0 0 0
## sample_TGACCA_Nel1 0 0 0 1 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 1 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 1 0 0 1 0 0
## sample_CGATGT_Alt1 0 0 0 1 0 0 0
## sample_CTGTA_Alt14 1 0 0 1 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 1 0 0 0
## sample_GCCAAT_Alt4 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 1 0 0 0
## sample_TTAGGC_Alt6 0 0 0 1 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 NA NA NA 0 0
## sample_ACAAA_Sub1 0 0 0 0 1 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 1 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 1 0 0
## sample_CGATGT_Sub6 0 NA 0 0 1 0 0
## sample_CTTGCTT_Sub14 0 0 NA NA NA 0 0
## sample_GAATTCA_Sub9 0 1 0 0 1 0 0
## sample_GGACCTA_Sub10 0 1 0 0 0 0 0
## sample_GTATT_Sub12 0 NA 0 0 NA 0 0
## sample_TGACCA_Sub2 0 NA 0 0 NA 0 0
## sample_ACAGTG_Cau2 0 NA NA NA NA 0 0
## sample_ACAGTG_Cau3 0 0 1 1 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 NA NA 0 1 0
## sample_ATGAAAC_Cau12 0 0 0 0 NA 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 1 0
## sample_CTGTA_Cau8 0 0 0 0 NA 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 1 0
## sample_TCACC_Cau4 0 0 NA NA 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 NA 0 0
## sample_AAAAGTT_Div13 0 0 NA NA 0 0 0
## sample_ACTAT_Div14 0 0 NA NA 0 0 0
## sample_AGCAT_Div11 0 0 NA NA NA 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 NA NA 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 1 0
## sample_CTTGCTT_Div15 0 0 NA NA NA 0 0
## sample_GTATT_Div10 0 0 0 0 NA 0 0
## sample_GTATT_Div7 0 0 0 0 NA 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1096] [,1097] [,1098] [,1099] [,1100] [,1101] [,1102]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 NA NA NA 0 0
## sample_CTAGC_Nel7 1 0 1 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 1
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 1 0 0 0 0 1 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 1 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 1 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 1 0 0 0 0
## sample_CGATGT_Alt1 0 0 1 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 1 0 0 0 0
## sample_GCCAAT_Alt9 0 0 1 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 1
## sample_AAAAGTT_Sub15 0 NA 0 0 0 NA 0
## sample_ACAAA_Sub1 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 1
## sample_AGCAT_Sub13 0 0 0 0 0 1 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 NA 0 0 0 NA 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 1 1
## sample_GGACCTA_Sub10 0 0 0 0 0 0 1
## sample_GTATT_Sub12 0 0 0 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 1 0
## sample_ACAGTG_Cau2 0 1 0 0 1 0 0
## sample_ACAGTG_Cau3 0 1 0 0 0 0 0
## sample_ACTAT_Cau11 0 1 0 0 0 0 0
## sample_ACTAT_Cau9 0 1 0 0 0 0 0
## sample_AGCCC_Cau7 0 NA 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 NA 0 0 0 0 0
## sample_CTAGC_Cau5 0 1 0 0 0 0 0
## sample_CTGTA_Cau8 0 1 0 0 1 0 0
## sample_GGACCTA_Cau13 0 1 0 0 0 0 0
## sample_TCACC_Cau1 0 1 0 0 0 0 0
## sample_TCACC_Cau4 0 1 0 0 0 0 0
## sample_TGACCA_Cau6 0 1 0 0 0 0 0
## sample_AAAAGTT_Div12 0 1 0 0 0 0 0
## sample_AAAAGTT_Div13 0 1 0 0 0 0 0
## sample_ACTAT_Div14 0 1 0 0 0 0 0
## sample_AGCAT_Div11 0 1 0 0 1 0 0
## sample_AGCCC_Div9 0 1 0 0 0 0 0
## sample_ATCACG_Div1 0 1 0 1 1 0 0
## sample_ATGAAAC_Div8 0 1 0 0 0 0 0
## sample_CGATGT_Div3 0 1 0 0 1 0 0
## sample_CTAGC_Div2 0 1 0 0 0 0 0
## sample_CTTGA_Div6 0 1 0 0 0 0 0
## sample_CTTGCTT_Div15 0 1 0 0 0 0 NA
## sample_GTATT_Div10 0 1 0 0 0 0 NA
## sample_GTATT_Div7 0 1 0 0 0 0 0
## sample_TGACCA_Div5 0 1 0 0 0 0 0
## sample_TTAGGC_Div4 0 1 NA NA NA 0 0
## [,1103] [,1104] [,1105] [,1106] [,1107] [,1108] [,1109]
## sample_ACAAA_Nel3 0 0 0 0 0 1 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 1 NA
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 1 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 NA
## sample_GGACCTA_Nel11 0 1 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 1 NA
## sample_AAAAGTT_Alt12 0 0 0 0 0 1 0
## sample_ACAAA_Alt11 0 0 0 0 0 1 0
## sample_ACAGTG_Alt3 0 0 0 1 1 1 0
## sample_AGCCC_Alt13 0 0 0 1 1 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 1 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 1 0
## sample_CTGTA_Alt14 0 1 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 1 0
## sample_GAATTCA_Alt15 0 0 0 0 0 1 0
## sample_GCCAAT_Alt4 1 0 0 0 0 1 0
## sample_GCCAAT_Alt9 0 0 0 0 0 1 0
## sample_TTAGGC_Alt2 1 0 0 0 0 1 0
## sample_TTAGGC_Alt6 0 0 0 0 0 1 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 NA 0 0 0 NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 1 NA
## sample_ACTAT_Sub7 0 0 0 0 0 1 NA
## sample_AGCAT_Sub13 0 0 0 0 0 1 0
## sample_AGCCC_Sub11 0 0 NA NA NA 1 0
## sample_CGATGT_Sub6 0 NA 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 NA NA NA NA 1 0
## sample_GAATTCA_Sub9 0 0 0 0 0 1 0
## sample_GGACCTA_Sub10 0 0 0 0 0 1 0
## sample_GTATT_Sub12 0 NA NA NA NA 1 NA
## sample_TGACCA_Sub2 0 0 0 0 0 1 0
## sample_ACAGTG_Cau2 0 NA NA NA NA 0 0
## sample_ACAGTG_Cau3 0 NA 1 0 0 0 1
## sample_ACTAT_Cau11 0 0 1 0 0 0 0
## sample_ACTAT_Cau9 0 0 1 0 0 0 0
## sample_AGCCC_Cau7 0 0 1 0 0 1 0
## sample_ATGAAAC_Cau12 0 NA 1 0 0 0 0
## sample_CTAGC_Cau5 0 0 1 0 0 0 0
## sample_CTGTA_Cau8 0 NA 1 0 0 NA 0
## sample_GGACCTA_Cau13 0 0 1 0 0 0 0
## sample_TCACC_Cau1 0 0 1 0 0 0 0
## sample_TCACC_Cau4 0 0 NA NA NA 0 0
## sample_TGACCA_Cau6 0 0 1 0 0 0 0
## sample_AAAAGTT_Div12 0 0 1 0 0 0 0
## sample_AAAAGTT_Div13 0 0 1 0 0 0 0
## sample_ACTAT_Div14 0 0 1 0 0 0 0
## sample_AGCAT_Div11 0 0 NA NA NA 0 0
## sample_AGCCC_Div9 0 0 1 0 0 0 0
## sample_ATCACG_Div1 0 0 1 0 0 0 NA
## sample_ATGAAAC_Div8 0 0 1 0 0 0 0
## sample_CGATGT_Div3 0 0 1 0 0 0 0
## sample_CTAGC_Div2 0 0 1 0 0 0 0
## sample_CTTGA_Div6 0 0 1 0 0 0 0
## sample_CTTGCTT_Div15 0 0 1 0 0 0 0
## sample_GTATT_Div10 0 0 1 0 0 0 0
## sample_GTATT_Div7 0 0 1 0 0 0 0
## sample_TGACCA_Div5 0 0 1 0 0 0 0
## sample_TTAGGC_Div4 0 0 1 0 0 0 0
## [,1110] [,1111] [,1112] [,1113] [,1114] [,1115] [,1116]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 1 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 1 0 0
## sample_CGATGT_Nel4 1 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 1 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 1 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 1 0 0 0 0
## sample_GGACCTA_Nel13 1 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 1 0 1 0 0
## sample_ACAAA_Alt11 1 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 1 0 0 0 0
## sample_AGCCC_Alt13 1 0 0 0 0 0 0
## sample_ATCACG_Alt5 1 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 1 0 0 0 0
## sample_CGATGT_Alt1 1 0 1 0 0 0 0
## sample_CTGTA_Alt14 1 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 1 0 0 0 0
## sample_GAATTCA_Alt15 1 0 1 0 0 0 0
## sample_GCCAAT_Alt4 0 0 1 0 0 0 0
## sample_GCCAAT_Alt9 1 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 1 0 NA NA NA NA NA
## sample_ACAAA_Sub1 1 0 NA NA 0 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 NA NA 0
## sample_CGATGT_Sub6 NA NA 0 0 NA NA 0
## sample_CTTGCTT_Sub14 NA NA NA NA 0 0 NA
## sample_GAATTCA_Sub9 0 0 1 0 1 0 0
## sample_GGACCTA_Sub10 1 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 NA NA NA NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 NA
## sample_ACAGTG_Cau2 0 0 0 0 0 0 NA
## sample_ACAGTG_Cau3 0 0 0 0 0 0 1
## sample_ACTAT_Cau11 0 0 0 0 0 0 1
## sample_ACTAT_Cau9 0 0 0 0 0 0 1
## sample_AGCCC_Cau7 0 0 0 0 0 0 1
## sample_ATGAAAC_Cau12 0 0 0 0 NA NA 1
## sample_CTAGC_Cau5 0 0 0 0 0 0 1
## sample_CTGTA_Cau8 0 0 NA NA NA NA NA
## sample_GGACCTA_Cau13 0 0 0 0 NA NA 1
## sample_TCACC_Cau1 0 0 0 0 0 0 1
## sample_TCACC_Cau4 0 0 0 0 0 0 1
## sample_TGACCA_Cau6 0 0 0 0 0 0 1
## sample_AAAAGTT_Div12 0 0 0 0 NA NA 1
## sample_AAAAGTT_Div13 0 0 0 0 0 0 1
## sample_ACTAT_Div14 0 0 0 0 0 0 1
## sample_AGCAT_Div11 0 0 0 0 NA NA NA
## sample_AGCCC_Div9 0 0 0 0 0 0 1
## sample_ATCACG_Div1 0 0 0 0 0 0 NA
## sample_ATGAAAC_Div8 0 0 0 0 0 0 NA
## sample_CGATGT_Div3 0 0 0 0 0 0 1
## sample_CTAGC_Div2 0 1 0 0 0 0 NA
## sample_CTTGA_Div6 0 1 0 0 0 0 1
## sample_CTTGCTT_Div15 0 0 NA NA NA NA NA
## sample_GTATT_Div10 0 0 0 0 0 0 NA
## sample_GTATT_Div7 0 0 0 0 0 0 NA
## sample_TGACCA_Div5 0 0 0 0 0 1 1
## sample_TTAGGC_Div4 0 0 0 1 0 0 1
## [,1117] [,1118] [,1119] [,1120] [,1121] [,1122] [,1123]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 1 0 0 0
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 1 0 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 1 0 0 0
## sample_CGATGT_Alt1 0 0 1 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 1 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 1 0 0 0
## sample_AAAAGTT_Sub15 NA NA 0 0 NA NA NA
## sample_ACAAA_Sub1 0 NA 1 0 0 0 NA
## sample_ACTAT_Sub7 0 0 0 1 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 NA
## sample_CGATGT_Sub6 NA 0 0 0 0 0 NA
## sample_CTTGCTT_Sub14 0 NA NA 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 NA 1 NA NA 0
## sample_TGACCA_Sub2 0 0 NA 0 0 0 0
## sample_ACAGTG_Cau2 1 0 0 0 1 0 0
## sample_ACAGTG_Cau3 1 0 0 0 1 1 0
## sample_ACTAT_Cau11 1 1 0 0 1 1 0
## sample_ACTAT_Cau9 1 1 0 0 1 1 0
## sample_AGCCC_Cau7 1 0 0 0 1 1 NA
## sample_ATGAAAC_Cau12 1 NA 0 0 1 1 0
## sample_CTAGC_Cau5 1 1 0 0 1 1 0
## sample_CTGTA_Cau8 NA NA 0 0 1 1 NA
## sample_GGACCTA_Cau13 1 0 0 0 1 1 0
## sample_TCACC_Cau1 1 1 0 0 1 1 0
## sample_TCACC_Cau4 1 0 0 0 1 1 0
## sample_TGACCA_Cau6 1 1 0 0 1 1 0
## sample_AAAAGTT_Div12 1 1 0 0 1 1 0
## sample_AAAAGTT_Div13 1 1 0 0 1 1 0
## sample_ACTAT_Div14 1 0 0 0 1 1 0
## sample_AGCAT_Div11 1 0 0 0 1 1 0
## sample_AGCCC_Div9 1 1 0 0 1 1 0
## sample_ATCACG_Div1 1 1 0 0 1 1 0
## sample_ATGAAAC_Div8 1 0 0 0 1 1 0
## sample_CGATGT_Div3 1 0 0 0 1 1 0
## sample_CTAGC_Div2 1 0 0 0 1 1 0
## sample_CTTGA_Div6 1 1 0 0 1 1 0
## sample_CTTGCTT_Div15 1 0 0 0 1 1 0
## sample_GTATT_Div10 1 1 0 0 1 1 0
## sample_GTATT_Div7 1 1 0 0 1 1 0
## sample_TGACCA_Div5 1 0 0 0 1 1 0
## sample_TTAGGC_Div4 1 1 0 0 1 1 0
## [,1124] [,1125] [,1126] [,1127] [,1128] [,1129] [,1130]
## sample_ACAAA_Nel3 0 0 1 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 1 0 0
## sample_AGCAT_Nel8 0 0 1 0 0 0 0
## sample_ATGAAAC_Nel10 1 0 0 0 1 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 1 0 0
## sample_CGATGT_Nel4 0 0 0 0 1 1 0
## sample_CTAGC_Nel7 0 0 1 0 0 0 0
## sample_CTGTA_Nel12 1 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 1 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 1 0 0
## sample_GTATT_Nel14 0 0 0 0 1 0 0
## sample_TCACC_Nel6 0 0 0 0 1 0 0
## sample_TGACCA_Nel1 0 0 0 0 1 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 1 0 1 0 0
## sample_AGCCC_Alt13 0 0 1 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 1 0 0
## sample_ATCACG_Alt7 1 0 1 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 1 0 0
## sample_CTGTA_Alt14 1 0 0 0 1 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 1 1 0 0 0
## sample_GCCAAT_Alt9 1 0 1 0 1 0 0
## sample_TTAGGC_Alt2 1 0 0 0 1 0 0
## sample_TTAGGC_Alt6 0 0 0 0 1 0 0
## sample_TTAGGC_Alt8 1 0 0 0 1 0 0
## sample_AAAAGTT_Sub15 0 NA NA NA NA 0 NA
## sample_ACAAA_Sub1 0 0 0 0 1 0 0
## sample_ACTAT_Sub7 0 0 0 0 1 0 0
## sample_AGCAT_Sub13 0 0 0 0 1 0 0
## sample_AGCCC_Sub11 0 NA NA 0 NA 0 0
## sample_CGATGT_Sub6 0 0 0 0 NA 0 NA
## sample_CTTGCTT_Sub14 0 0 0 NA 1 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 1 0 1
## sample_GGACCTA_Sub10 0 0 1 0 1 0 0
## sample_GTATT_Sub12 0 0 0 0 NA 0 NA
## sample_TGACCA_Sub2 0 1 1 0 1 0 0
## sample_ACAGTG_Cau2 0 1 0 0 0 0 0
## sample_ACAGTG_Cau3 0 1 1 0 0 0 0
## sample_ACTAT_Cau11 0 1 0 0 0 0 0
## sample_ACTAT_Cau9 0 1 0 0 0 0 0
## sample_AGCCC_Cau7 0 NA NA 0 0 0 0
## sample_ATGAAAC_Cau12 0 1 1 0 0 0 0
## sample_CTAGC_Cau5 0 1 0 0 0 0 0
## sample_CTGTA_Cau8 0 NA NA 0 NA 0 0
## sample_GGACCTA_Cau13 0 1 0 0 0 0 0
## sample_TCACC_Cau1 0 1 1 0 0 0 0
## sample_TCACC_Cau4 0 NA NA 0 0 0 0
## sample_TGACCA_Cau6 0 1 0 0 0 0 0
## sample_AAAAGTT_Div12 0 1 0 0 0 0 0
## sample_AAAAGTT_Div13 0 1 0 0 0 0 0
## sample_ACTAT_Div14 0 1 0 0 0 0 0
## sample_AGCAT_Div11 0 1 0 0 0 0 0
## sample_AGCCC_Div9 0 NA NA 0 0 0 0
## sample_ATCACG_Div1 0 1 0 0 0 0 0
## sample_ATGAAAC_Div8 0 1 1 0 0 0 0
## sample_CGATGT_Div3 0 1 1 0 0 0 0
## sample_CTAGC_Div2 0 1 0 0 0 0 0
## sample_CTTGA_Div6 0 1 0 0 0 0 0
## sample_CTTGCTT_Div15 0 1 0 0 0 0 0
## sample_GTATT_Div10 0 1 1 0 0 0 0
## sample_GTATT_Div7 0 1 1 0 0 0 0
## sample_TGACCA_Div5 0 1 0 0 0 0 0
## sample_TTAGGC_Div4 0 1 1 0 0 0 0
## [,1131] [,1132] [,1133] [,1134] [,1135] [,1136] [,1137]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 1 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 1
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 1 0
## sample_TGACCA_Nel1 0 1 0 0 0 0 1
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 1
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 1 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 1 0 0 0 0 0
## sample_CGATGT_Alt1 0 1 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 1 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 1 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 1 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 NA NA 0 0 0 NA
## sample_ACAAA_Sub1 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 NA
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 1 0 0 NA
## sample_ACAGTG_Cau3 0 0 0 1 0 0 0
## sample_ACTAT_Cau11 0 0 0 1 1 0 0
## sample_ACTAT_Cau9 1 0 1 1 0 0 0
## sample_AGCCC_Cau7 1 0 NA 1 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 1 0 0 NA
## sample_CTAGC_Cau5 0 0 0 1 0 0 0
## sample_CTGTA_Cau8 0 0 0 1 0 0 0
## sample_GGACCTA_Cau13 0 0 0 1 0 0 0
## sample_TCACC_Cau1 1 0 0 1 0 0 0
## sample_TCACC_Cau4 1 0 0 1 0 0 NA
## sample_TGACCA_Cau6 0 0 0 1 0 0 0
## sample_AAAAGTT_Div12 1 0 0 1 0 0 0
## sample_AAAAGTT_Div13 0 0 0 1 0 0 0
## sample_ACTAT_Div14 1 0 0 1 0 0 0
## sample_AGCAT_Div11 0 0 0 1 0 0 NA
## sample_AGCCC_Div9 0 0 0 1 1 0 0
## sample_ATCACG_Div1 0 0 0 1 0 0 0
## sample_ATGAAAC_Div8 0 0 0 1 1 0 0
## sample_CGATGT_Div3 0 0 0 1 0 0 0
## sample_CTAGC_Div2 1 0 0 1 0 0 0
## sample_CTTGA_Div6 1 0 0 1 0 0 0
## sample_CTTGCTT_Div15 0 0 0 1 0 0 0
## sample_GTATT_Div10 0 0 0 1 0 0 0
## sample_GTATT_Div7 0 0 0 1 0 0 0
## sample_TGACCA_Div5 0 0 0 1 0 0 0
## sample_TTAGGC_Div4 1 0 0 1 0 0 0
## [,1138] [,1139] [,1140] [,1141] [,1142] [,1143] [,1144]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 1 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 1 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 1
## sample_TCACC_Nel6 0 0 0 1 0 0 0
## sample_TGACCA_Nel1 1 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 1 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 1 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 1 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 1 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 1 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA 0 0
## sample_ACAAA_Sub1 0 NA NA 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 NA 0 0 0 0
## sample_CGATGT_Sub6 0 NA 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 1 0 0 0 0
## sample_GTATT_Sub12 NA NA 0 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 NA 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 NA NA 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 NA NA 0 0 0 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0
## sample_ACTAT_Div14 NA 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 1 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 0
## sample_GTATT_Div10 0 0 0 0 0 0 0
## sample_GTATT_Div7 NA 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1145] [,1146] [,1147] [,1148] [,1149] [,1150] [,1151]
## sample_ACAAA_Nel3 0 0 1 0 0 1 0
## sample_ACAGTG_Nel5 0 0 0 0 0 1 0
## sample_AGCAT_Nel8 0 0 1 0 0 1 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 1 0
## sample_ATGAAAC_Nel15 0 0 1 0 0 1 0
## sample_CGATGT_Nel4 1 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 1 0
## sample_CTGTA_Nel12 0 0 0 0 0 1 0
## sample_CTGTA_Nel9 0 0 0 0 0 1 0
## sample_CTTGA_Nel2 0 0 1 0 0 1 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 1 0 1 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 1 0
## sample_TGACCA_Nel1 0 0 1 0 0 1 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 1 0
## sample_ACAAA_Alt11 0 0 0 0 0 1 0
## sample_ACAGTG_Alt3 0 0 0 0 0 1 0
## sample_AGCCC_Alt13 0 0 0 0 1 1 0
## sample_ATCACG_Alt5 0 0 0 0 0 1 0
## sample_ATCACG_Alt7 0 0 0 0 1 1 0
## sample_CGATGT_Alt1 0 0 0 0 1 1 0
## sample_CTGTA_Alt14 0 0 1 0 0 1 0
## sample_CTTGA_Alt10 0 0 0 0 0 1 0
## sample_GAATTCA_Alt15 0 0 NA NA 0 1 0
## sample_GCCAAT_Alt4 0 0 1 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 1 0
## sample_TTAGGC_Alt2 0 0 0 0 0 1 0
## sample_TTAGGC_Alt6 0 0 1 1 0 0 0
## sample_TTAGGC_Alt8 0 0 NA 0 0 1 0
## sample_AAAAGTT_Sub15 NA 0 0 0 NA NA 0
## sample_ACAAA_Sub1 0 0 0 0 0 1 0
## sample_ACTAT_Sub7 0 0 NA NA 0 1 0
## sample_AGCAT_Sub13 0 0 0 0 0 1 0
## sample_AGCCC_Sub11 0 0 0 0 0 1 0
## sample_CGATGT_Sub6 NA 0 0 0 NA NA 0
## sample_CTTGCTT_Sub14 0 0 1 0 0 1 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 1 0
## sample_GTATT_Sub12 NA 0 0 0 NA NA 0
## sample_TGACCA_Sub2 0 0 1 0 0 1 0
## sample_ACAGTG_Cau2 0 0 1 1 0 0 NA
## sample_ACAGTG_Cau3 0 0 1 1 0 0 0
## sample_ACTAT_Cau11 0 0 1 1 0 0 1
## sample_ACTAT_Cau9 0 0 1 1 0 0 1
## sample_AGCCC_Cau7 0 0 0 1 0 0 1
## sample_ATGAAAC_Cau12 0 0 1 1 0 0 1
## sample_CTAGC_Cau5 0 0 1 1 0 0 1
## sample_CTGTA_Cau8 NA NA NA NA NA NA 1
## sample_GGACCTA_Cau13 0 0 0 1 0 0 0
## sample_TCACC_Cau1 0 0 1 1 0 0 0
## sample_TCACC_Cau4 0 0 1 1 0 0 NA
## sample_TGACCA_Cau6 0 0 1 1 0 0 1
## sample_AAAAGTT_Div12 0 0 1 1 0 0 1
## sample_AAAAGTT_Div13 0 0 1 1 0 0 1
## sample_ACTAT_Div14 0 0 1 1 0 0 0
## sample_AGCAT_Div11 NA 0 NA NA 0 0 1
## sample_AGCCC_Div9 0 0 1 1 0 0 1
## sample_ATCACG_Div1 0 0 1 1 0 0 0
## sample_ATGAAAC_Div8 0 0 1 1 0 0 1
## sample_CGATGT_Div3 0 0 1 1 0 0 1
## sample_CTAGC_Div2 0 0 1 1 0 0 1
## sample_CTTGA_Div6 0 0 1 1 0 0 1
## sample_CTTGCTT_Div15 NA 0 1 1 0 0 1
## sample_GTATT_Div10 0 0 1 1 0 0 0
## sample_GTATT_Div7 0 0 1 1 0 0 0
## sample_TGACCA_Div5 0 0 1 1 0 0 0
## sample_TTAGGC_Div4 0 1 1 1 0 0 1
## [,1152] [,1153] [,1154] [,1155] [,1156] [,1157] [,1158]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 1 0 0
## sample_AGCAT_Nel8 0 0 0 0 1 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 1 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 1 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 1 0
## sample_CTAGC_Nel7 0 0 0 0 1 1 0
## sample_CTGTA_Nel12 0 0 0 0 1 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 1 0
## sample_CTTGA_Nel2 0 0 0 0 1 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 1 1 0
## sample_GTATT_Nel14 0 0 0 0 1 1 0
## sample_TCACC_Nel6 0 0 0 0 1 1 0
## sample_TGACCA_Nel1 0 0 0 0 1 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 1
## sample_ACAAA_Alt11 0 0 0 0 1 0 0
## sample_ACAGTG_Alt3 0 0 0 0 1 0 0
## sample_AGCCC_Alt13 0 0 0 0 1 1 0
## sample_ATCACG_Alt5 0 0 0 0 1 0 0
## sample_ATCACG_Alt7 0 0 0 0 1 1 0
## sample_CGATGT_Alt1 0 0 0 0 1 0 1
## sample_CTGTA_Alt14 0 0 0 0 1 0 0
## sample_CTTGA_Alt10 0 0 0 0 1 0 0
## sample_GAATTCA_Alt15 0 0 0 0 1 0 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0
## sample_GCCAAT_Alt9 0 0 0 0 1 1 1
## sample_TTAGGC_Alt2 0 0 0 0 0 0 1
## sample_TTAGGC_Alt6 0 0 0 0 1 0 0
## sample_TTAGGC_Alt8 0 0 0 0 1 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 NA 0 NA
## sample_ACAAA_Sub1 0 0 0 NA NA 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 1 0 0
## sample_AGCCC_Sub11 0 0 0 0 NA 0 0
## sample_CGATGT_Sub6 0 0 0 NA NA 0 0
## sample_CTTGCTT_Sub14 0 0 0 NA 1 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 1 0 0
## sample_GTATT_Sub12 0 0 0 NA NA 0 0
## sample_TGACCA_Sub2 0 0 0 NA 1 0 0
## sample_ACAGTG_Cau2 NA NA NA 1 0 0 0
## sample_ACAGTG_Cau3 0 1 0 1 0 0 0
## sample_ACTAT_Cau11 0 1 0 1 0 0 0
## sample_ACTAT_Cau9 0 1 0 1 0 0 0
## sample_AGCCC_Cau7 0 1 0 1 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 1 0 0 0
## sample_CTAGC_Cau5 0 1 0 1 0 0 0
## sample_CTGTA_Cau8 0 0 0 NA 0 NA NA
## sample_GGACCTA_Cau13 0 1 0 1 0 0 0
## sample_TCACC_Cau1 1 1 1 1 0 0 0
## sample_TCACC_Cau4 NA NA NA 1 0 0 0
## sample_TGACCA_Cau6 0 1 0 1 0 0 0
## sample_AAAAGTT_Div12 0 0 0 1 0 0 0
## sample_AAAAGTT_Div13 0 1 0 1 0 0 0
## sample_ACTAT_Div14 1 1 1 1 0 0 0
## sample_AGCAT_Div11 0 0 0 1 0 0 0
## sample_AGCCC_Div9 0 0 0 1 0 0 0
## sample_ATCACG_Div1 1 1 1 1 0 0 0
## sample_ATGAAAC_Div8 0 1 0 1 0 0 0
## sample_CGATGT_Div3 0 1 0 1 0 0 0
## sample_CTAGC_Div2 0 1 0 1 0 0 0
## sample_CTTGA_Div6 0 0 0 1 0 0 0
## sample_CTTGCTT_Div15 0 0 0 1 0 0 0
## sample_GTATT_Div10 1 1 1 1 0 0 0
## sample_GTATT_Div7 0 1 0 1 0 0 0
## sample_TGACCA_Div5 1 1 1 1 0 0 0
## sample_TTAGGC_Div4 0 1 0 1 0 0 0
## [,1159] [,1160] [,1161] [,1162] [,1163] [,1164] [,1165]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 NA 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 1 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 1 0 0
## sample_CTTGA_Nel2 0 0 0 0 1 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 NA 0 0
## sample_TCACC_Nel6 0 0 0 0 NA 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0
## sample_ACAAA_Alt11 0 0 0 0 NA 0 0
## sample_ACAGTG_Alt3 1 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 1 0 0
## sample_ATCACG_Alt5 0 0 0 0 1 0 0
## sample_ATCACG_Alt7 0 0 0 0 1 0 0
## sample_CGATGT_Alt1 0 0 0 0 1 0 0
## sample_CTGTA_Alt14 0 0 0 0 1 0 0
## sample_CTTGA_Alt10 0 0 0 0 1 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 NA 0 0
## sample_TTAGGC_Alt2 0 0 0 0 1 0 0
## sample_TTAGGC_Alt6 0 0 0 0 1 0 0
## sample_TTAGGC_Alt8 0 0 0 1 1 0 0
## sample_AAAAGTT_Sub15 0 0 0 NA NA 0 0
## sample_ACAAA_Sub1 0 0 0 NA 0 0 0
## sample_ACTAT_Sub7 0 0 0 1 0 0 0
## sample_AGCAT_Sub13 0 0 0 1 0 0 0
## sample_AGCCC_Sub11 NA 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 NA 0 0 0 0
## sample_CTTGCTT_Sub14 NA 0 0 0 NA 0 0
## sample_GAATTCA_Sub9 0 0 1 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 1 0 0 0
## sample_GTATT_Sub12 NA 0 NA NA NA 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 NA 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 1 0 NA 0 NA NA
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 NA 0 0 0 NA 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 1 0 0 0 0 0
## sample_AAAAGTT_Div13 0 1 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 1 0 0 0 0 0
## sample_AGCCC_Div9 0 1 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 1 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 1 1
## sample_CTTGCTT_Div15 0 1 0 0 0 0 0
## sample_GTATT_Div10 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1166] [,1167] [,1168] [,1169] [,1170] [,1171] [,1172]
## sample_ACAAA_Nel3 1 0 0 0 1 0 0
## sample_ACAGTG_Nel5 0 0 1 0 1 0 0
## sample_AGCAT_Nel8 0 0 1 0 1 0 0
## sample_ATGAAAC_Nel10 1 0 0 0 1 0 0
## sample_ATGAAAC_Nel15 1 0 1 0 1 0 0
## sample_CGATGT_Nel4 1 0 0 0 1 0 0
## sample_CTAGC_Nel7 0 0 1 0 1 0 0
## sample_CTGTA_Nel12 NA 0 1 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 1 0 0
## sample_CTTGA_Nel2 0 0 1 0 1 0 0
## sample_GGACCTA_Nel11 0 0 1 0 1 0 0
## sample_GGACCTA_Nel13 0 0 1 0 1 0 0
## sample_GTATT_Nel14 0 0 1 0 1 0 0
## sample_TCACC_Nel6 0 0 1 0 1 0 0
## sample_TGACCA_Nel1 1 0 1 0 1 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0
## sample_ACAAA_Alt11 0 0 0 0 1 0 1
## sample_ACAGTG_Alt3 1 0 1 0 1 0 0
## sample_AGCCC_Alt13 0 0 1 0 1 0 0
## sample_ATCACG_Alt5 1 0 1 0 1 0 0
## sample_ATCACG_Alt7 0 0 1 0 1 0 0
## sample_CGATGT_Alt1 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 1 0 1 0 0
## sample_CTTGA_Alt10 0 0 0 0 1 0 0
## sample_GAATTCA_Alt15 0 0 1 0 1 0 0
## sample_GCCAAT_Alt4 0 0 1 0 0 0 0
## sample_GCCAAT_Alt9 0 0 1 0 1 0 0
## sample_TTAGGC_Alt2 1 0 1 0 1 0 0
## sample_TTAGGC_Alt6 0 0 1 0 1 0 0
## sample_TTAGGC_Alt8 1 0 NA NA 1 1 0
## sample_AAAAGTT_Sub15 NA 0 0 0 0 NA NA
## sample_ACAAA_Sub1 0 0 NA NA 1 NA 0
## sample_ACTAT_Sub7 1 0 0 0 1 0 0
## sample_AGCAT_Sub13 1 0 1 0 1 0 0
## sample_AGCCC_Sub11 1 0 0 0 1 0 0
## sample_CGATGT_Sub6 0 0 0 0 NA NA NA
## sample_CTTGCTT_Sub14 1 NA 0 0 1 0 0
## sample_GAATTCA_Sub9 1 0 0 0 1 0 0
## sample_GGACCTA_Sub10 1 0 1 0 1 0 0
## sample_GTATT_Sub12 1 0 NA NA NA NA 0
## sample_TGACCA_Sub2 1 1 NA NA 1 0 0
## sample_ACAGTG_Cau2 0 1 0 0 0 NA NA
## sample_ACAGTG_Cau3 0 1 0 0 0 0 0
## sample_ACTAT_Cau11 0 1 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 1 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 NA NA NA 0 0 0
## sample_CTAGC_Cau5 0 1 0 1 0 0 0
## sample_CTGTA_Cau8 0 NA NA NA 0 NA 0
## sample_GGACCTA_Cau13 0 1 0 1 0 0 0
## sample_TCACC_Cau1 0 1 0 0 0 0 0
## sample_TCACC_Cau4 0 1 0 0 0 0 0
## sample_TGACCA_Cau6 0 1 0 1 0 0 0
## sample_AAAAGTT_Div12 0 1 0 1 0 0 0
## sample_AAAAGTT_Div13 0 1 0 1 0 0 0
## sample_ACTAT_Div14 0 1 0 1 0 0 0
## sample_AGCAT_Div11 0 1 0 0 0 0 0
## sample_AGCCC_Div9 0 1 0 0 0 0 0
## sample_ATCACG_Div1 0 1 0 0 0 0 0
## sample_ATGAAAC_Div8 0 1 NA NA 0 0 0
## sample_CGATGT_Div3 0 1 0 0 0 0 0
## sample_CTAGC_Div2 0 1 0 0 0 0 0
## sample_CTTGA_Div6 0 1 0 0 0 0 0
## sample_CTTGCTT_Div15 0 1 NA NA 0 NA NA
## sample_GTATT_Div10 0 1 0 1 0 0 0
## sample_GTATT_Div7 0 1 0 0 NA NA 0
## sample_TGACCA_Div5 0 1 0 1 0 0 0
## sample_TTAGGC_Div4 0 1 0 0 0 0 0
## [,1173] [,1174] [,1175] [,1176] [,1177] [,1178] [,1179]
## sample_ACAAA_Nel3 0 0 0 0 0 0 1
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 1 0 0 0
## sample_CGATGT_Nel4 0 0 0 1 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 NA
## sample_CTGTA_Nel12 0 0 0 0 0 1 NA
## sample_CTGTA_Nel9 0 0 0 1 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 1 0 0 0
## sample_GGACCTA_Nel13 0 0 0 1 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 1 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 1
## sample_AAAAGTT_Alt12 0 0 0 1 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 NA
## sample_ATCACG_Alt5 0 0 0 1 0 0 0
## sample_ATCACG_Alt7 0 0 0 1 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 1 0 0 0
## sample_CTTGA_Alt10 0 1 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 1 0 0 0
## sample_GCCAAT_Alt4 0 0 0 1 0 0 0
## sample_GCCAAT_Alt9 0 0 0 1 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA 0 0 0 NA
## sample_ACAAA_Sub1 0 0 NA 0 0 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 1 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 NA
## sample_CGATGT_Sub6 NA NA 0 0 0 0 NA
## sample_CTTGCTT_Sub14 0 NA 0 0 NA 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA NA NA 0 0 0
## sample_TGACCA_Sub2 0 0 0 1 0 0 0
## sample_ACAGTG_Cau2 NA NA 0 0 1 0 0
## sample_ACAGTG_Cau3 0 0 0 0 1 0 0
## sample_ACTAT_Cau11 0 0 0 0 1 0 0
## sample_ACTAT_Cau9 0 0 0 0 1 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 1 0 0
## sample_CTAGC_Cau5 0 0 0 0 1 0 0
## sample_CTGTA_Cau8 0 0 NA 0 1 NA NA
## sample_GGACCTA_Cau13 0 0 0 0 1 0 NA
## sample_TCACC_Cau1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 1 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 1 0 0 0 1 0 0
## sample_AAAAGTT_Div13 0 0 0 0 1 0 0
## sample_ACTAT_Div14 0 0 0 0 1 0 0
## sample_AGCAT_Div11 0 NA 0 0 1 0 0
## sample_AGCCC_Div9 0 0 0 0 1 0 0
## sample_ATCACG_Div1 0 0 1 0 1 0 0
## sample_ATGAAAC_Div8 0 0 0 0 1 0 0
## sample_CGATGT_Div3 0 0 0 0 1 0 0
## sample_CTAGC_Div2 0 0 0 0 1 0 0
## sample_CTTGA_Div6 0 0 0 0 1 0 0
## sample_CTTGCTT_Div15 0 NA NA 0 1 0 0
## sample_GTATT_Div10 NA 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 1 0 0
## sample_TGACCA_Div5 0 0 0 0 1 0 0
## sample_TTAGGC_Div4 0 0 0 0 1 0 0
## [,1180] [,1181] [,1182] [,1183] [,1184] [,1185] [,1186]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 1 1 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 1 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 1 0 0 1 0
## sample_CGATGT_Nel4 0 0 1 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 1 1
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 1 0 1 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 1
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 1 0 0 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 1 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 1 1 0 1 0
## sample_CTTGA_Alt10 0 0 1 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 1 0 0 0 0
## sample_TTAGGC_Alt2 0 0 1 1 0 0 0
## sample_TTAGGC_Alt6 0 0 1 0 0 0 0
## sample_TTAGGC_Alt8 0 0 1 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 NA 0 0 0 NA
## sample_ACAAA_Sub1 0 0 1 0 0 0 0
## sample_ACTAT_Sub7 0 0 1 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 1 0
## sample_AGCCC_Sub11 0 1 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 NA
## sample_CTTGCTT_Sub14 0 1 0 0 0 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 1 0
## sample_GGACCTA_Sub10 0 0 1 0 0 1 0
## sample_GTATT_Sub12 0 0 NA 0 0 0 0
## sample_TGACCA_Sub2 0 0 1 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 1 0 0 0 1 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 0 0 0 NA
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 0
## sample_GTATT_Div10 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 0 0 NA
## sample_TGACCA_Div5 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1187] [,1188] [,1189] [,1190] [,1191] [,1192] [,1193]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 1 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 1 0 0 0 0 0
## sample_GGACCTA_Nel13 1 0 0 0 0 1 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 1 0
## sample_ATCACG_Alt7 0 0 0 NA 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 1 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 1 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 1 0
## sample_TTAGGC_Alt8 0 0 0 0 0 1 0
## sample_AAAAGTT_Sub15 0 NA NA 0 NA NA 0
## sample_ACAAA_Sub1 0 NA NA 0 0 1 NA
## sample_ACTAT_Sub7 0 0 0 1 0 0 0
## sample_AGCAT_Sub13 1 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 NA NA 0
## sample_CGATGT_Sub6 0 0 0 NA 0 0 0
## sample_CTTGCTT_Sub14 0 NA NA 0 NA NA 0
## sample_GAATTCA_Sub9 0 0 0 NA 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA NA NA NA 1 0
## sample_TGACCA_Sub2 0 0 0 0 0 NA 0
## sample_ACAGTG_Cau2 1 NA NA NA 0 0 1
## sample_ACAGTG_Cau3 0 NA NA 0 NA 0 1
## sample_ACTAT_Cau11 0 0 1 0 0 0 1
## sample_ACTAT_Cau9 0 0 0 0 0 0 1
## sample_AGCCC_Cau7 0 0 0 0 NA 0 1
## sample_ATGAAAC_Cau12 1 0 0 0 NA 0 1
## sample_CTAGC_Cau5 0 0 0 0 0 0 1
## sample_CTGTA_Cau8 1 NA NA 0 NA 0 1
## sample_GGACCTA_Cau13 1 0 0 0 0 0 1
## sample_TCACC_Cau1 1 0 0 0 0 0 1
## sample_TCACC_Cau4 1 0 0 0 0 0 1
## sample_TGACCA_Cau6 1 0 0 0 0 0 1
## sample_AAAAGTT_Div12 0 0 0 0 0 0 1
## sample_AAAAGTT_Div13 1 0 0 0 1 0 1
## sample_ACTAT_Div14 0 0 0 0 0 0 1
## sample_AGCAT_Div11 0 0 0 0 0 0 1
## sample_AGCCC_Div9 0 0 0 NA 0 0 1
## sample_ATCACG_Div1 1 0 0 NA 0 0 1
## sample_ATGAAAC_Div8 0 0 0 0 0 0 1
## sample_CGATGT_Div3 1 0 0 0 0 0 1
## sample_CTAGC_Div2 1 0 0 0 0 0 1
## sample_CTTGA_Div6 1 0 0 NA 0 0 1
## sample_CTTGCTT_Div15 1 NA NA 0 0 0 1
## sample_GTATT_Div10 1 0 1 0 0 0 1
## sample_GTATT_Div7 0 0 0 0 NA 0 1
## sample_TGACCA_Div5 0 0 0 0 0 0 1
## sample_TTAGGC_Div4 0 0 0 0 0 0 1
## [,1194] [,1195] [,1196] [,1197] [,1198] [,1199] [,1200]
## sample_ACAAA_Nel3 1 1 0 0 0 0 0
## sample_ACAGTG_Nel5 0 1 0 0 1 0 0
## sample_AGCAT_Nel8 1 0 0 0 1 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 1 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 1 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 1 0 0
## sample_ATCACG_Alt7 1 0 0 0 0 0 0
## sample_CGATGT_Alt1 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 1 0 0 0 0 0 0
## sample_GAATTCA_Alt15 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 1 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA 0 0 0
## sample_ACAAA_Sub1 1 0 NA 0 NA NA 0
## sample_ACTAT_Sub7 1 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 1 0 NA 0 0 0 0
## sample_CGATGT_Sub6 1 0 0 0 NA NA 0
## sample_CTTGCTT_Sub14 1 0 0 0 0 0 NA
## sample_GAATTCA_Sub9 1 0 0 0 0 0 0
## sample_GGACCTA_Sub10 1 0 0 0 NA NA 0
## sample_GTATT_Sub12 1 0 0 0 0 0 NA
## sample_TGACCA_Sub2 1 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 1 0 0 0 NA
## sample_ACAGTG_Cau3 0 0 1 0 0 0 NA
## sample_ACTAT_Cau11 0 0 1 0 0 0 0
## sample_ACTAT_Cau9 0 0 1 0 0 0 0
## sample_AGCCC_Cau7 0 0 1 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 1 1 0 0 0
## sample_CTAGC_Cau5 0 0 1 0 0 0 0
## sample_CTGTA_Cau8 NA NA NA NA 0 0 NA
## sample_GGACCTA_Cau13 0 0 1 0 NA NA 0
## sample_TCACC_Cau1 0 0 1 0 0 0 0
## sample_TCACC_Cau4 0 0 1 1 0 0 0
## sample_TGACCA_Cau6 0 0 1 0 0 0 0
## sample_AAAAGTT_Div12 0 0 1 0 0 0 0
## sample_AAAAGTT_Div13 0 0 1 0 0 0 0
## sample_ACTAT_Div14 0 0 1 0 0 0 0
## sample_AGCAT_Div11 0 0 1 0 0 0 0
## sample_AGCCC_Div9 0 0 1 1 0 0 1
## sample_ATCACG_Div1 0 0 1 0 0 0 1
## sample_ATGAAAC_Div8 0 0 1 0 0 0 0
## sample_CGATGT_Div3 0 0 1 0 0 0 0
## sample_CTAGC_Div2 0 0 1 0 0 0 0
## sample_CTTGA_Div6 0 0 1 0 0 0 0
## sample_CTTGCTT_Div15 0 0 1 0 0 0 0
## sample_GTATT_Div10 0 0 1 0 0 0 0
## sample_GTATT_Div7 0 0 1 NA 0 0 0
## sample_TGACCA_Div5 0 0 1 0 0 0 0
## sample_TTAGGC_Div4 0 0 1 0 0 0 0
## [,1201] [,1202] [,1203] [,1204] [,1205] [,1206] [,1207]
## sample_ACAAA_Nel3 0 0 1 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 1 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 1 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 1 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 1 0 0
## sample_CTAGC_Nel7 0 0 1 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 1 0 0
## sample_CTGTA_Nel9 0 0 1 0 1 0 0
## sample_CTTGA_Nel2 0 0 1 0 0 0 0
## sample_GGACCTA_Nel11 0 0 1 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 1 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 1 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 1 0 1 0 0
## sample_ATCACG_Alt5 0 0 1 0 1 0 0
## sample_ATCACG_Alt7 0 0 1 0 1 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 1 0 0 0 0
## sample_CTTGA_Alt10 0 0 1 0 1 0 0
## sample_GAATTCA_Alt15 0 0 1 0 0 0 0
## sample_GCCAAT_Alt4 0 0 1 0 0 0 0
## sample_GCCAAT_Alt9 0 0 1 0 1 0 0
## sample_TTAGGC_Alt2 0 0 1 0 0 0 0
## sample_TTAGGC_Alt6 0 0 1 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 1 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 0 NA NA
## sample_ACAAA_Sub1 0 NA NA NA 0 0 0
## sample_ACTAT_Sub7 0 0 1 0 0 0 0
## sample_AGCAT_Sub13 0 0 1 0 0 0 0
## sample_AGCCC_Sub11 0 NA NA 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 NA 0
## sample_CTTGCTT_Sub14 0 0 0 NA 0 0 0
## sample_GAATTCA_Sub9 0 0 1 0 0 0 0
## sample_GGACCTA_Sub10 0 0 1 0 0 0 0
## sample_GTATT_Sub12 0 NA NA 0 NA 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 NA 0 1 0
## sample_ACAGTG_Cau3 0 0 0 1 0 1 1
## sample_ACTAT_Cau11 0 1 0 1 0 0 1
## sample_ACTAT_Cau9 0 NA NA 1 0 1 0
## sample_AGCCC_Cau7 0 0 0 1 0 1 1
## sample_ATGAAAC_Cau12 0 0 0 1 0 1 NA
## sample_CTAGC_Cau5 0 0 0 1 0 1 0
## sample_CTGTA_Cau8 NA 0 0 1 0 NA NA
## sample_GGACCTA_Cau13 0 0 0 1 0 0 NA
## sample_TCACC_Cau1 0 0 0 1 0 0 1
## sample_TCACC_Cau4 0 0 0 1 0 1 1
## sample_TGACCA_Cau6 0 0 0 1 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 1 0 0 1
## sample_ACTAT_Div14 0 0 0 1 0 0 1
## sample_AGCAT_Div11 0 0 0 1 0 1 1
## sample_AGCCC_Div9 1 0 0 0 0 1 1
## sample_ATCACG_Div1 0 0 0 0 0 1 1
## sample_ATGAAAC_Div8 0 0 0 1 0 0 1
## sample_CGATGT_Div3 0 0 0 1 0 0 1
## sample_CTAGC_Div2 0 0 0 1 0 0 1
## sample_CTTGA_Div6 0 0 0 1 0 0 1
## sample_CTTGCTT_Div15 0 NA NA 1 0 0 1
## sample_GTATT_Div10 0 0 0 1 0 1 NA
## sample_GTATT_Div7 0 0 0 1 0 0 0
## sample_TGACCA_Div5 0 0 0 1 0 0 1
## sample_TTAGGC_Div4 0 0 0 1 0 1 1
## [,1208] [,1209] [,1210] [,1211] [,1212] [,1213] [,1214]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 NA 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 NA 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 1 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 1 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 1 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 1 NA NA NA NA
## sample_ACAAA_Sub1 0 NA 1 NA NA 0 0
## sample_ACTAT_Sub7 0 0 1 0 0 0 0
## sample_AGCAT_Sub13 0 0 1 0 0 0 0
## sample_AGCCC_Sub11 0 0 1 0 0 0 0
## sample_CGATGT_Sub6 0 0 NA 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 NA 0 0 0 0
## sample_GAATTCA_Sub9 0 0 1 0 0 0 0
## sample_GGACCTA_Sub10 0 0 1 0 0 0 0
## sample_GTATT_Sub12 0 0 1 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 1 0 0 0 0 1
## sample_ACAGTG_Cau3 1 1 0 NA NA 0 1
## sample_ACTAT_Cau11 0 1 0 0 0 0 1
## sample_ACTAT_Cau9 1 1 0 0 0 0 1
## sample_AGCCC_Cau7 0 0 0 1 1 0 1
## sample_ATGAAAC_Cau12 0 1 0 NA NA 0 1
## sample_CTAGC_Cau5 0 1 0 0 0 0 1
## sample_CTGTA_Cau8 0 1 0 NA NA 0 1
## sample_GGACCTA_Cau13 0 1 0 NA NA 0 1
## sample_TCACC_Cau1 0 1 0 0 0 0 1
## sample_TCACC_Cau4 0 1 0 0 1 NA 1
## sample_TGACCA_Cau6 1 1 0 0 0 0 1
## sample_AAAAGTT_Div12 0 1 0 0 1 0 1
## sample_AAAAGTT_Div13 1 1 0 0 1 0 1
## sample_ACTAT_Div14 0 1 0 0 0 0 1
## sample_AGCAT_Div11 0 1 0 0 0 0 1
## sample_AGCCC_Div9 0 1 0 0 1 0 1
## sample_ATCACG_Div1 1 1 0 0 0 0 1
## sample_ATGAAAC_Div8 0 1 0 NA NA 0 1
## sample_CGATGT_Div3 0 1 0 0 1 0 1
## sample_CTAGC_Div2 0 1 0 0 1 0 1
## sample_CTTGA_Div6 0 1 0 1 1 0 1
## sample_CTTGCTT_Div15 0 1 0 NA NA 0 1
## sample_GTATT_Div10 0 1 0 0 1 0 1
## sample_GTATT_Div7 0 1 0 NA NA 0 1
## sample_TGACCA_Div5 0 1 0 0 0 0 1
## sample_TTAGGC_Div4 0 1 0 0 1 0 1
## [,1215] [,1216] [,1217] [,1218] [,1219] [,1220] [,1221]
## sample_ACAAA_Nel3 1 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 1 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 1 0 0 0 0
## sample_CGATGT_Nel4 0 0 1 0 0 0 NA
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 NA
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 1 0 0 1 NA
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 NA
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 1 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 1 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 1 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 1 0 0 0 NA
## sample_GCCAAT_Alt4 0 0 1 0 0 0 0
## sample_GCCAAT_Alt9 0 0 1 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 1 0 0 1 0
## sample_AAAAGTT_Sub15 NA NA 1 0 NA NA 0
## sample_ACAAA_Sub1 NA NA NA 0 NA NA 0
## sample_ACTAT_Sub7 0 0 1 0 0 1 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 NA
## sample_AGCCC_Sub11 0 NA NA 0 NA NA 0
## sample_CGATGT_Sub6 0 0 NA 0 0 0 NA
## sample_CTTGCTT_Sub14 NA 0 0 0 NA NA 0
## sample_GAATTCA_Sub9 0 0 0 0 1 0 0
## sample_GGACCTA_Sub10 0 0 1 0 0 0 0
## sample_GTATT_Sub12 NA 0 1 0 NA NA 0
## sample_TGACCA_Sub2 0 0 1 0 0 0 0
## sample_ACAGTG_Cau2 NA NA 0 0 1 0 NA
## sample_ACAGTG_Cau3 0 1 0 0 1 0 1
## sample_ACTAT_Cau11 0 0 0 0 1 0 1
## sample_ACTAT_Cau9 0 0 0 0 1 0 1
## sample_AGCCC_Cau7 0 0 0 0 1 0 1
## sample_ATGAAAC_Cau12 NA NA 0 0 1 0 1
## sample_CTAGC_Cau5 0 1 0 0 1 0 1
## sample_CTGTA_Cau8 NA NA 0 0 1 0 1
## sample_GGACCTA_Cau13 0 NA 0 0 1 0 1
## sample_TCACC_Cau1 0 0 0 0 1 0 1
## sample_TCACC_Cau4 NA 0 0 0 1 0 1
## sample_TGACCA_Cau6 0 1 0 0 1 0 1
## sample_AAAAGTT_Div12 0 0 0 0 1 0 1
## sample_AAAAGTT_Div13 0 0 0 0 1 0 1
## sample_ACTAT_Div14 0 1 0 0 1 0 1
## sample_AGCAT_Div11 NA 1 0 0 1 0 1
## sample_AGCCC_Div9 0 0 0 0 1 0 1
## sample_ATCACG_Div1 0 0 0 0 1 0 1
## sample_ATGAAAC_Div8 0 0 0 0 1 0 1
## sample_CGATGT_Div3 0 1 0 0 1 0 1
## sample_CTAGC_Div2 0 0 0 0 1 0 1
## sample_CTTGA_Div6 0 0 0 0 1 0 1
## sample_CTTGCTT_Div15 NA 1 0 0 1 0 1
## sample_GTATT_Div10 NA 0 0 0 1 0 1
## sample_GTATT_Div7 NA NA 0 0 1 0 1
## sample_TGACCA_Div5 0 1 0 0 1 0 1
## sample_TTAGGC_Div4 0 0 0 0 1 0 1
## [,1222] [,1223] [,1224] [,1225] [,1226] [,1227] [,1228]
## sample_ACAAA_Nel3 0 0 0 0 0 0 1
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 1
## sample_CGATGT_Nel4 0 0 0 0 0 0 1
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 1
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 0 0 0 0 1
## sample_GGACCTA_Nel13 0 0 0 0 0 0 1
## sample_GTATT_Nel14 0 0 0 0 0 0 1
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 1
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 1
## sample_ACAGTG_Alt3 0 0 0 0 0 0 1
## sample_AGCCC_Alt13 0 0 0 0 0 0 1
## sample_ATCACG_Alt5 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 1
## sample_CTGTA_Alt14 0 0 0 0 0 0 1
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 1
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 1
## sample_TTAGGC_Alt8 0 0 0 0 0 0 1
## sample_AAAAGTT_Sub15 NA NA 0 NA 0 0 1
## sample_ACAAA_Sub1 0 0 0 0 0 0 1
## sample_ACTAT_Sub7 0 0 0 0 0 0 1
## sample_AGCAT_Sub13 0 1 0 0 0 0 1
## sample_AGCCC_Sub11 0 0 0 0 0 0 1
## sample_CGATGT_Sub6 0 0 0 NA 0 0 NA
## sample_CTTGCTT_Sub14 0 0 0 NA NA 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 1
## sample_GGACCTA_Sub10 0 0 0 0 0 0 1
## sample_GTATT_Sub12 0 0 0 0 NA 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 NA
## sample_ACAGTG_Cau2 1 0 0 1 NA 0 0
## sample_ACAGTG_Cau3 NA NA 0 1 0 1 0
## sample_ACTAT_Cau11 1 0 0 1 0 0 0
## sample_ACTAT_Cau9 1 0 0 1 0 1 0
## sample_AGCCC_Cau7 NA NA 0 NA 0 0 0
## sample_ATGAAAC_Cau12 1 0 0 NA 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 1 0
## sample_CTGTA_Cau8 NA NA 0 NA 0 0 0
## sample_GGACCTA_Cau13 1 0 0 1 0 0 0
## sample_TCACC_Cau1 0 0 1 1 0 1 0
## sample_TCACC_Cau4 0 0 0 1 NA 0 0
## sample_TGACCA_Cau6 1 0 0 0 0 1 0
## sample_AAAAGTT_Div12 1 0 0 1 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 1 0
## sample_ACTAT_Div14 1 0 0 1 0 0 0
## sample_AGCAT_Div11 0 0 0 1 NA 0 0
## sample_AGCCC_Div9 1 0 0 1 0 1 0
## sample_ATCACG_Div1 1 0 0 1 0 1 0
## sample_ATGAAAC_Div8 1 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 1 1 0 0 0
## sample_CTAGC_Div2 1 0 0 0 1 0 0
## sample_CTTGA_Div6 0 0 0 1 0 0 0
## sample_CTTGCTT_Div15 NA NA 0 NA 1 0 0
## sample_GTATT_Div10 0 0 0 1 0 1 0
## sample_GTATT_Div7 0 0 1 1 0 0 0
## sample_TGACCA_Div5 0 0 0 0 1 0 0
## sample_TTAGGC_Div4 1 0 0 1 0 1 0
## [,1229] [,1230] [,1231] [,1232] [,1233] [,1234] [,1235]
## sample_ACAAA_Nel3 0 0 0 0 0 0 1
## sample_ACAGTG_Nel5 0 0 0 0 0 0 1
## sample_AGCAT_Nel8 0 0 0 0 0 0 1
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 1
## sample_CTGTA_Nel12 0 1 0 0 0 1 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 1
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 1
## sample_GGACCTA_Nel13 0 1 0 0 0 0 1
## sample_GTATT_Nel14 0 0 0 0 0 0 1
## sample_TCACC_Nel6 1 0 0 0 0 1 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 1
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 1 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 1
## sample_ATCACG_Alt5 0 0 0 1 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 1 0 1 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 1
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 1 1 0 1
## sample_TTAGGC_Alt8 0 0 0 0 0 0 1
## sample_AAAAGTT_Sub15 0 0 NA 0 NA NA NA
## sample_ACAAA_Sub1 0 0 0 1 NA 1 1
## sample_ACTAT_Sub7 0 0 0 0 1 1 1
## sample_AGCAT_Sub13 0 0 0 0 0 1 0
## sample_AGCCC_Sub11 0 0 NA 0 NA NA 0
## sample_CGATGT_Sub6 NA NA 0 0 NA 1 NA
## sample_CTTGCTT_Sub14 NA NA NA 1 1 NA 1
## sample_GAATTCA_Sub9 0 0 0 1 0 0 1
## sample_GGACCTA_Sub10 0 0 0 0 1 0 0
## sample_GTATT_Sub12 NA NA 0 0 NA 0 1
## sample_TGACCA_Sub2 NA NA 0 0 1 0 NA
## sample_ACAGTG_Cau2 0 0 0 0 1 0 0
## sample_ACAGTG_Cau3 0 0 0 1 1 0 0
## sample_ACTAT_Cau11 0 0 0 1 1 0 0
## sample_ACTAT_Cau9 0 0 0 1 1 0 0
## sample_AGCCC_Cau7 0 0 0 1 1 0 0
## sample_ATGAAAC_Cau12 0 0 NA 0 1 0 0
## sample_CTAGC_Cau5 0 0 0 0 1 0 0
## sample_CTGTA_Cau8 0 0 NA 0 1 0 0
## sample_GGACCTA_Cau13 0 0 0 0 1 0 0
## sample_TCACC_Cau1 0 0 0 0 1 0 0
## sample_TCACC_Cau4 0 0 NA 0 1 0 0
## sample_TGACCA_Cau6 0 0 0 0 1 0 0
## sample_AAAAGTT_Div12 0 0 0 0 1 0 0
## sample_AAAAGTT_Div13 0 0 0 0 1 0 0
## sample_ACTAT_Div14 0 0 0 0 1 0 0
## sample_AGCAT_Div11 0 0 0 0 1 0 0
## sample_AGCCC_Div9 0 0 0 0 1 0 0
## sample_ATCACG_Div1 0 0 0 0 1 0 0
## sample_ATGAAAC_Div8 0 0 0 0 1 0 0
## sample_CGATGT_Div3 0 0 0 0 1 0 0
## sample_CTAGC_Div2 0 0 0 0 1 0 0
## sample_CTTGA_Div6 0 0 0 0 1 0 0
## sample_CTTGCTT_Div15 0 0 0 0 1 0 NA
## sample_GTATT_Div10 0 0 0 0 1 0 NA
## sample_GTATT_Div7 0 0 0 0 1 0 0
## sample_TGACCA_Div5 0 0 1 0 1 0 0
## sample_TTAGGC_Div4 0 0 0 0 1 0 0
## [,1236] [,1237] [,1238] [,1239] [,1240] [,1241] [,1242]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 1 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 1 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 1 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 1 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 NA NA NA NA NA 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 1 0 0 0
## sample_TTAGGC_Alt8 0 0 0 1 0 0 0
## sample_AAAAGTT_Sub15 NA 0 0 0 0 0 NA
## sample_ACAAA_Sub1 NA 0 0 0 0 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 1 0
## sample_CGATGT_Sub6 0 0 0 0 1 0 0
## sample_CTTGCTT_Sub14 0 0 0 0 0 0 NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 0 0 0 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA 0 0 0 0 1 NA
## sample_ACAGTG_Cau3 0 0 0 0 0 1 1
## sample_ACTAT_Cau11 0 0 0 0 0 1 0
## sample_ACTAT_Cau9 0 0 0 0 0 1 0
## sample_AGCCC_Cau7 0 0 0 0 0 1 1
## sample_ATGAAAC_Cau12 0 0 0 0 0 1 NA
## sample_CTAGC_Cau5 0 0 0 0 0 1 0
## sample_CTGTA_Cau8 NA 0 0 0 0 1 1
## sample_GGACCTA_Cau13 0 0 0 0 0 1 0
## sample_TCACC_Cau1 0 1 0 0 0 1 0
## sample_TCACC_Cau4 0 0 0 0 0 1 0
## sample_TGACCA_Cau6 0 0 0 0 0 1 0
## sample_AAAAGTT_Div12 0 0 0 0 0 1 0
## sample_AAAAGTT_Div13 0 0 0 0 0 1 0
## sample_ACTAT_Div14 0 0 0 0 0 1 1
## sample_AGCAT_Div11 0 0 0 0 0 1 0
## sample_AGCCC_Div9 0 0 0 0 0 1 0
## sample_ATCACG_Div1 0 0 0 0 0 1 1
## sample_ATGAAAC_Div8 0 0 0 0 0 1 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 1 1
## sample_CTTGA_Div6 0 0 0 0 0 1 0
## sample_CTTGCTT_Div15 NA 0 0 0 0 1 NA
## sample_GTATT_Div10 0 0 0 0 0 1 0
## sample_GTATT_Div7 0 0 0 0 0 1 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1243] [,1244] [,1245] [,1246] [,1247] [,1248] [,1249]
## sample_ACAAA_Nel3 0 1 0 0 0 0 0
## sample_ACAGTG_Nel5 0 1 0 0 0 0 0
## sample_AGCAT_Nel8 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 1 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 1 0 0 0 0 0
## sample_CGATGT_Nel4 0 1 1 0 0 0 0
## sample_CTAGC_Nel7 0 1 0 0 0 0 0
## sample_CTGTA_Nel12 0 1 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 1 0 0 0 0 0
## sample_GGACCTA_Nel11 0 1 0 0 0 0 0
## sample_GGACCTA_Nel13 0 1 0 0 0 0 0
## sample_GTATT_Nel14 0 1 0 0 0 0 0
## sample_TCACC_Nel6 0 1 0 0 0 0 0
## sample_TGACCA_Nel1 0 1 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 1 0 0 0 0 0
## sample_ACAAA_Alt11 0 1 0 0 0 0 0
## sample_ACAGTG_Alt3 0 1 0 0 0 0 0
## sample_AGCCC_Alt13 0 1 0 0 0 0 0
## sample_ATCACG_Alt5 0 1 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 1 0 0
## sample_CGATGT_Alt1 0 1 0 0 0 0 0
## sample_CTGTA_Alt14 0 1 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 1 0 0
## sample_GCCAAT_Alt4 0 1 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 1 0 0 0 0 0
## sample_TTAGGC_Alt6 0 1 0 0 0 0 0
## sample_TTAGGC_Alt8 0 1 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA 0 0 0
## sample_ACAAA_Sub1 NA 1 0 0 0 0 0
## sample_ACTAT_Sub7 0 1 0 0 0 0 0
## sample_AGCAT_Sub13 0 1 0 0 0 0 0
## sample_AGCCC_Sub11 1 1 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA 1 0 0 0 0 0
## sample_GAATTCA_Sub9 0 1 0 0 0 0 0
## sample_GGACCTA_Sub10 0 1 0 0 0 0 0
## sample_GTATT_Sub12 NA NA NA NA 0 0 0
## sample_TGACCA_Sub2 0 NA NA NA 0 0 0
## sample_ACAGTG_Cau2 NA NA NA NA NA 0 1
## sample_ACAGTG_Cau3 0 0 0 1 0 0 1
## sample_ACTAT_Cau11 1 0 0 1 0 0 1
## sample_ACTAT_Cau9 1 0 0 1 0 0 1
## sample_AGCCC_Cau7 0 0 0 1 0 0 1
## sample_ATGAAAC_Cau12 NA NA NA NA 0 0 1
## sample_CTAGC_Cau5 1 0 0 1 0 0 1
## sample_CTGTA_Cau8 0 0 0 1 0 0 1
## sample_GGACCTA_Cau13 0 0 0 1 0 0 1
## sample_TCACC_Cau1 0 0 0 1 0 0 1
## sample_TCACC_Cau4 1 1 0 0 0 0 1
## sample_TGACCA_Cau6 1 0 0 1 0 0 1
## sample_AAAAGTT_Div12 1 0 0 1 0 0 1
## sample_AAAAGTT_Div13 1 0 0 1 0 0 1
## sample_ACTAT_Div14 0 0 0 1 0 0 1
## sample_AGCAT_Div11 1 NA NA NA 0 0 1
## sample_AGCCC_Div9 1 0 0 1 0 0 1
## sample_ATCACG_Div1 0 0 0 1 0 0 1
## sample_ATGAAAC_Div8 1 0 0 1 0 0 1
## sample_CGATGT_Div3 1 0 0 1 0 0 1
## sample_CTAGC_Div2 0 0 0 1 0 0 1
## sample_CTTGA_Div6 0 0 0 1 0 0 1
## sample_CTTGCTT_Div15 NA NA NA NA 0 0 1
## sample_GTATT_Div10 1 0 0 1 0 0 1
## sample_GTATT_Div7 0 0 0 1 0 1 1
## sample_TGACCA_Div5 0 0 0 1 0 0 1
## sample_TTAGGC_Div4 1 0 0 1 0 0 1
## [,1250] [,1251] [,1252] [,1253] [,1254] [,1255] [,1256]
## sample_ACAAA_Nel3 0 0 1 0 0 0 0
## sample_ACAGTG_Nel5 0 0 1 0 1 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 1 0 1 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 1 0 0 0 0
## sample_CGATGT_Nel4 0 0 1 0 0 0 0
## sample_CTAGC_Nel7 0 0 1 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 1 0 1 0 0 0 0
## sample_CTTGA_Nel2 0 0 1 0 0 0 0
## sample_GGACCTA_Nel11 0 0 1 0 0 0 0
## sample_GGACCTA_Nel13 0 0 1 0 0 0 0
## sample_GTATT_Nel14 1 0 1 0 0 0 NA
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 1 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 1 0 0 0 0
## sample_ACAAA_Alt11 0 0 1 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 NA
## sample_ATCACG_Alt5 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 NA
## sample_CGATGT_Alt1 1 0 1 0 0 0 0
## sample_CTGTA_Alt14 0 0 1 0 0 0 NA
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 1 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 1 0 0 0 0
## sample_TTAGGC_Alt2 0 0 1 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA 0 0 NA NA NA 0
## sample_ACAAA_Sub1 0 0 1 0 0 0 0
## sample_ACTAT_Sub7 0 0 1 1 0 0 NA
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 NA NA 0 0 0 NA
## sample_CGATGT_Sub6 0 0 1 NA 0 0 0
## sample_CTTGCTT_Sub14 0 0 1 NA NA NA NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 1 0 0 0 0
## sample_GTATT_Sub12 0 NA NA 0 NA NA NA
## sample_TGACCA_Sub2 0 0 1 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 NA NA 0
## sample_ACAGTG_Cau3 0 0 0 0 0 1 NA
## sample_ACTAT_Cau11 0 1 0 0 0 0 1
## sample_ACTAT_Cau9 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 NA NA 0
## sample_ATGAAAC_Cau12 0 0 0 0 NA NA 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 0 NA NA NA
## sample_GGACCTA_Cau13 0 0 0 0 0 1 0
## sample_TCACC_Cau1 0 0 0 0 0 1 0
## sample_TCACC_Cau4 0 1 0 0 0 1 NA
## sample_TGACCA_Cau6 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 1 0
## sample_AAAAGTT_Div13 0 1 0 0 NA NA 0
## sample_ACTAT_Div14 0 0 0 0 0 1 0
## sample_AGCAT_Div11 0 0 0 0 0 1 0
## sample_AGCCC_Div9 0 0 0 0 0 1 0
## sample_ATCACG_Div1 0 0 0 0 0 1 0
## sample_ATGAAAC_Div8 0 0 0 0 NA NA 0
## sample_CGATGT_Div3 0 0 0 0 0 1 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 0 1 NA
## sample_CTTGCTT_Div15 0 0 0 0 NA NA NA
## sample_GTATT_Div10 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 NA NA 0
## sample_TGACCA_Div5 0 0 0 0 0 1 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1257] [,1258] [,1259] [,1260] [,1261] [,1262] [,1263]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 1 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 NA NA NA NA NA NA NA
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 NA NA NA NA NA NA NA
## sample_ATCACG_Alt5 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 NA NA NA NA NA NA NA
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 NA NA NA NA NA NA NA
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 1 0 0 0 1 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 1 0 0 0 1 1
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 0 0 0
## sample_ACAAA_Sub1 0 0 0 0 0 0 0
## sample_ACTAT_Sub7 NA NA NA NA NA NA NA
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 NA NA NA NA NA NA NA
## sample_CGATGT_Sub6 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA NA NA NA NA NA NA
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 1 0 0 0 1 1
## sample_GTATT_Sub12 NA NA NA NA NA NA NA
## sample_TGACCA_Sub2 1 1 1 1 0 1 1
## sample_ACAGTG_Cau2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau3 NA NA NA NA NA NA NA
## sample_ACTAT_Cau11 0 1 1 0 0 1 1
## sample_ACTAT_Cau9 1 0 0 0 0 1 1
## sample_AGCCC_Cau7 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 NA NA NA NA NA NA NA
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 NA NA NA NA NA NA NA
## sample_TGACCA_Cau6 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 0 0 0
## sample_AGCAT_Div11 1 1 1 1 0 1 1
## sample_AGCCC_Div9 0 1 1 0 0 1 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0
## sample_CTTGA_Div6 NA NA NA NA NA NA NA
## sample_CTTGCTT_Div15 NA NA NA NA NA NA NA
## sample_GTATT_Div10 1 0 0 0 0 1 1
## sample_GTATT_Div7 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 0 0 0 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1264] [,1265] [,1266] [,1267] [,1268] [,1269] [,1270]
## sample_ACAAA_Nel3 0 0 0 0 1 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 1 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 NA 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 NA 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 1 0 0
## sample_ATCACG_Alt7 NA 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 NA 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 1 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 NA NA NA
## sample_ACAAA_Sub1 0 0 0 0 NA 0 NA
## sample_ACTAT_Sub7 NA 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 NA 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 NA NA 0
## sample_CTTGCTT_Sub14 NA NA 0 0 NA 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 1 0 0 0 0 0 0
## sample_GTATT_Sub12 NA 0 0 0 0 NA 0
## sample_TGACCA_Sub2 1 0 0 0 0 NA 0
## sample_ACAGTG_Cau2 0 0 0 1 0 1 NA
## sample_ACAGTG_Cau3 NA 0 0 1 0 1 0
## sample_ACTAT_Cau11 NA 0 0 1 0 1 0
## sample_ACTAT_Cau9 1 0 0 1 0 1 0
## sample_AGCCC_Cau7 0 0 0 1 0 1 0
## sample_ATGAAAC_Cau12 0 0 0 1 NA NA 0
## sample_CTAGC_Cau5 0 0 0 1 0 1 0
## sample_CTGTA_Cau8 NA 0 0 1 0 NA 0
## sample_GGACCTA_Cau13 0 0 0 1 0 NA 0
## sample_TCACC_Cau1 0 0 1 1 0 1 0
## sample_TCACC_Cau4 NA 0 0 1 0 1 0
## sample_TGACCA_Cau6 0 0 0 1 0 1 0
## sample_AAAAGTT_Div12 0 0 0 1 0 1 0
## sample_AAAAGTT_Div13 0 0 0 1 0 1 0
## sample_ACTAT_Div14 0 0 0 1 0 1 0
## sample_AGCAT_Div11 1 0 0 1 0 1 0
## sample_AGCCC_Div9 0 0 0 1 0 1 0
## sample_ATCACG_Div1 0 0 0 1 0 1 1
## sample_ATGAAAC_Div8 0 0 0 1 0 1 0
## sample_CGATGT_Div3 0 0 0 1 0 1 0
## sample_CTAGC_Div2 0 0 0 1 0 1 0
## sample_CTTGA_Div6 NA 0 0 1 0 1 0
## sample_CTTGCTT_Div15 NA 0 0 1 NA 1 NA
## sample_GTATT_Div10 1 0 0 1 0 1 0
## sample_GTATT_Div7 0 0 0 1 NA 1 0
## sample_TGACCA_Div5 0 0 0 1 0 1 0
## sample_TTAGGC_Div4 0 0 0 1 0 1 0
## [,1271] [,1272] [,1273] [,1274] [,1275] [,1276] [,1277]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 1 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 1 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 1 0 0 0 1 0 1
## sample_CTGTA_Nel9 1 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 1 0 0 0 0 1
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 1 0 0 0 0 0 0
## sample_TGACCA_Nel1 1 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 1 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 NA NA NA 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 1 0 0 0 0 1 0
## sample_ATCACG_Alt5 1 0 0 0 0 0 0
## sample_ATCACG_Alt7 1 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 1 0 0 0 0 0 0
## sample_GCCAAT_Alt9 1 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 1 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA 0 1 1 0 0 0
## sample_ACAAA_Sub1 NA 0 0 0 0 0 0
## sample_ACTAT_Sub7 1 0 0 0 0 0 0
## sample_AGCAT_Sub13 1 0 0 0 0 0 0
## sample_AGCCC_Sub11 1 0 1 1 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 1 1 0 0 NA
## sample_GAATTCA_Sub9 1 0 0 0 0 0 0
## sample_GGACCTA_Sub10 1 0 1 1 0 0 0
## sample_GTATT_Sub12 0 0 0 0 0 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 NA 0 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 1 1 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 1 1 0 0 0
## sample_ATGAAAC_Cau12 0 0 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 0 0 0 0
## sample_GGACCTA_Cau13 0 0 1 1 0 NA 0
## sample_TCACC_Cau1 1 0 1 1 0 0 0
## sample_TCACC_Cau4 1 0 1 1 0 NA 0
## sample_TGACCA_Cau6 1 0 1 1 0 NA 0
## sample_AAAAGTT_Div12 0 0 1 1 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 1 1 0 0 0
## sample_AGCAT_Div11 0 0 0 0 0 0 0
## sample_AGCCC_Div9 0 0 1 1 0 0 0
## sample_ATCACG_Div1 0 0 1 1 0 0 0
## sample_ATGAAAC_Div8 1 0 1 1 0 0 0
## sample_CGATGT_Div3 0 0 1 1 0 0 0
## sample_CTAGC_Div2 1 0 0 0 0 0 0
## sample_CTTGA_Div6 1 0 1 1 0 0 0
## sample_CTTGCTT_Div15 NA 0 1 1 0 0 0
## sample_GTATT_Div10 1 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 1 1 0 NA 0
## sample_TGACCA_Div5 0 0 1 1 0 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1278] [,1279] [,1280] [,1281] [,1282] [,1283] [,1284]
## sample_ACAAA_Nel3 1 0 0 1 1 0 0
## sample_ACAGTG_Nel5 0 0 0 1 1 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 1 1 0 0
## sample_ATGAAAC_Nel15 1 0 0 0 1 0 0
## sample_CGATGT_Nel4 0 0 0 1 1 0 0
## sample_CTAGC_Nel7 0 0 1 1 0 0 0
## sample_CTGTA_Nel12 1 0 0 1 0 0 0
## sample_CTGTA_Nel9 0 0 0 1 1 1 0
## sample_CTTGA_Nel2 1 0 0 1 0 0 0
## sample_GGACCTA_Nel11 1 0 0 1 1 0 0
## sample_GGACCTA_Nel13 1 0 0 1 1 0 0
## sample_GTATT_Nel14 1 0 0 1 0 0 0
## sample_TCACC_Nel6 0 0 0 0 1 0 0
## sample_TGACCA_Nel1 1 1 0 0 1 0 0
## sample_AAAAGTT_Alt12 0 0 0 1 1 0 0
## sample_ACAAA_Alt11 1 0 1 1 0 0 0
## sample_ACAGTG_Alt3 1 0 0 1 1 0 0
## sample_AGCCC_Alt13 0 0 0 1 0 0 0
## sample_ATCACG_Alt5 1 0 0 1 0 0 0
## sample_ATCACG_Alt7 0 0 0 1 0 0 0
## sample_CGATGT_Alt1 1 0 1 1 1 0 1
## sample_CTGTA_Alt14 0 0 0 1 1 0 0
## sample_CTTGA_Alt10 0 0 0 1 1 0 0
## sample_GAATTCA_Alt15 1 0 0 1 0 0 1
## sample_GCCAAT_Alt4 1 0 1 1 1 0 0
## sample_GCCAAT_Alt9 0 0 0 1 1 0 1
## sample_TTAGGC_Alt2 0 0 0 1 0 0 1
## sample_TTAGGC_Alt6 1 0 1 1 0 0 0
## sample_TTAGGC_Alt8 1 0 0 1 0 NA NA
## sample_AAAAGTT_Sub15 NA NA 0 NA 0 0 0
## sample_ACAAA_Sub1 NA 0 0 1 0 0 0
## sample_ACTAT_Sub7 1 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 1 0 0 0
## sample_AGCCC_Sub11 1 NA 0 1 0 NA NA
## sample_CGATGT_Sub6 0 0 0 1 0 0 0
## sample_CTTGCTT_Sub14 0 NA 0 1 NA 0 0
## sample_GAATTCA_Sub9 0 0 0 1 0 0 0
## sample_GGACCTA_Sub10 1 0 0 1 0 0 0
## sample_GTATT_Sub12 NA NA 0 NA NA 0 0
## sample_TGACCA_Sub2 0 0 0 1 0 0 0
## sample_ACAGTG_Cau2 0 NA 0 0 NA 0 0
## sample_ACAGTG_Cau3 0 0 0 0 NA 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 0 0 0 0 0
## sample_ATGAAAC_Cau12 NA NA 0 0 NA 0 0
## sample_CTAGC_Cau5 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 0 0 NA 0 0
## sample_GGACCTA_Cau13 0 0 0 0 0 0 0
## sample_TCACC_Cau1 0 0 0 0 0 0 0
## sample_TCACC_Cau4 0 0 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 0
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 0
## sample_ACTAT_Div14 0 0 0 0 NA 0 0
## sample_AGCAT_Div11 0 0 0 0 NA 0 0
## sample_AGCCC_Div9 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 0 0 0 0
## sample_ATGAAAC_Div8 0 0 0 0 0 0 0
## sample_CGATGT_Div3 0 0 0 0 0 0 0
## sample_CTAGC_Div2 0 0 0 0 0 0 0
## sample_CTTGA_Div6 0 0 0 0 NA 0 0
## sample_CTTGCTT_Div15 0 0 0 0 0 0 0
## sample_GTATT_Div10 0 0 0 0 0 0 0
## sample_GTATT_Div7 0 0 0 0 NA 0 0
## sample_TGACCA_Div5 0 0 0 0 NA 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1285] [,1286] [,1287] [,1288] [,1289] [,1290] [,1291]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 1 1 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 NA 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA NA 0
## sample_ACAAA_Sub1 NA NA NA NA NA 0 0
## sample_ACTAT_Sub7 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 NA NA NA NA NA NA 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 NA NA NA NA NA NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 1 0 0 0 0 NA NA
## sample_ACAGTG_Cau3 1 0 0 0 0 0 1
## sample_ACTAT_Cau11 1 0 0 0 0 0 1
## sample_ACTAT_Cau9 1 0 0 0 0 1 1
## sample_AGCCC_Cau7 NA NA NA NA NA 0 1
## sample_ATGAAAC_Cau12 NA NA NA NA NA 0 1
## sample_CTAGC_Cau5 1 0 0 0 0 1 1
## sample_CTGTA_Cau8 NA NA NA NA NA NA NA
## sample_GGACCTA_Cau13 NA NA NA NA NA 0 1
## sample_TCACC_Cau1 1 0 0 0 0 0 1
## sample_TCACC_Cau4 1 0 0 0 0 0 1
## sample_TGACCA_Cau6 1 0 1 0 0 0 1
## sample_AAAAGTT_Div12 1 0 0 0 0 NA 1
## sample_AAAAGTT_Div13 1 0 1 0 0 0 1
## sample_ACTAT_Div14 1 0 0 0 0 NA 1
## sample_AGCAT_Div11 1 0 0 0 0 0 1
## sample_AGCCC_Div9 1 0 0 0 0 0 1
## sample_ATCACG_Div1 1 0 0 0 0 0 1
## sample_ATGAAAC_Div8 NA NA NA NA NA 0 1
## sample_CGATGT_Div3 1 0 0 0 0 0 1
## sample_CTAGC_Div2 1 0 0 0 0 0 1
## sample_CTTGA_Div6 1 0 0 0 0 0 1
## sample_CTTGCTT_Div15 1 0 0 0 0 0 1
## sample_GTATT_Div10 1 0 0 0 0 0 1
## sample_GTATT_Div7 1 0 0 0 0 NA 1
## sample_TGACCA_Div5 1 0 0 0 0 0 1
## sample_TTAGGC_Div4 1 1 1 0 0 0 1
## [,1292] [,1293] [,1294] [,1295] [,1296] [,1297] [,1298]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 1 0 1 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 NA 0 0
## sample_TCACC_Nel6 0 0 0 0 NA 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 NA 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 1 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 0 NA NA
## sample_ACAAA_Sub1 0 0 0 0 0 NA NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0 NA 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 NA NA NA NA 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 0 0 NA 0 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 NA NA 0 0 0
## sample_ACAGTG_Cau3 0 0 0 1 0 0 0
## sample_ACTAT_Cau11 0 0 0 1 0 0 0
## sample_ACTAT_Cau9 0 0 0 1 0 0 0
## sample_AGCCC_Cau7 0 0 0 NA 0 0 0
## sample_ATGAAAC_Cau12 0 0 NA NA 0 NA NA
## sample_CTAGC_Cau5 0 0 0 1 0 0 0
## sample_CTGTA_Cau8 0 0 NA NA 0 NA 0
## sample_GGACCTA_Cau13 0 0 0 1 0 0 0
## sample_TCACC_Cau1 0 0 0 1 0 0 1
## sample_TCACC_Cau4 0 0 0 1 0 0 0
## sample_TGACCA_Cau6 0 0 0 1 0 0 0
## sample_AAAAGTT_Div12 NA NA 0 1 0 0 0
## sample_AAAAGTT_Div13 0 0 0 1 0 0 0
## sample_ACTAT_Div14 0 0 0 1 0 0 0
## sample_AGCAT_Div11 NA NA NA NA 0 0 0
## sample_AGCCC_Div9 0 0 0 1 0 0 0
## sample_ATCACG_Div1 0 0 0 1 0 0 0
## sample_ATGAAAC_Div8 0 0 0 1 0 0 0
## sample_CGATGT_Div3 0 0 0 1 0 0 0
## sample_CTAGC_Div2 0 0 0 1 0 0 0
## sample_CTTGA_Div6 0 0 0 1 0 0 0
## sample_CTTGCTT_Div15 NA NA 0 1 0 0 0
## sample_GTATT_Div10 0 0 0 1 0 0 0
## sample_GTATT_Div7 0 1 0 1 0 0 0
## sample_TGACCA_Div5 0 0 0 1 0 0 0
## sample_TTAGGC_Div4 0 0 0 1 0 1 0
## [,1299] [,1300] [,1301] [,1302] [,1303] [,1304] [,1305]
## sample_ACAAA_Nel3 0 0 0 0 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 1 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 1
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 0 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 1 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 1 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 1
## sample_CTTGA_Alt10 1 0 0 0 0 0 0
## sample_GAATTCA_Alt15 1 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 1 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 NA 0 0 1 NA
## sample_ACAAA_Sub1 0 0 NA 0 0 0 NA
## sample_ACTAT_Sub7 0 0 0 0 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 1
## sample_AGCCC_Sub11 0 0 0 0 0 0 NA
## sample_CGATGT_Sub6 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 0 NA 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 0 NA NA NA NA 0
## sample_TGACCA_Sub2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 NA NA NA NA 0
## sample_ACAGTG_Cau3 0 0 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 1 0 0
## sample_ACTAT_Cau9 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 NA NA NA NA 0
## sample_ATGAAAC_Cau12 0 0 NA 1 0 0 NA
## sample_CTAGC_Cau5 0 0 0 0 0 0 0
## sample_CTGTA_Cau8 0 0 NA 0 0 0 NA
## sample_GGACCTA_Cau13 0 0 NA 0 0 0 NA
## sample_TCACC_Cau1 0 0 0 1 0 0 0
## sample_TCACC_Cau4 0 0 0 1 0 0 0
## sample_TGACCA_Cau6 0 0 0 0 0 0 NA
## sample_AAAAGTT_Div12 0 0 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0 0 NA
## sample_ACTAT_Div14 0 0 0 0 1 0 0
## sample_AGCAT_Div11 0 0 0 NA NA NA NA
## sample_AGCCC_Div9 0 0 0 0 0 0 0
## sample_ATCACG_Div1 0 0 0 1 0 0 0
## sample_ATGAAAC_Div8 0 0 0 1 0 0 0
## sample_CGATGT_Div3 0 0 0 1 0 0 0
## sample_CTAGC_Div2 0 0 0 NA NA NA 0
## sample_CTTGA_Div6 0 0 0 0 1 0 0
## sample_CTTGCTT_Div15 0 0 0 NA NA NA NA
## sample_GTATT_Div10 0 0 0 0 0 0 NA
## sample_GTATT_Div7 0 0 0 0 0 0 0
## sample_TGACCA_Div5 0 1 0 0 1 0 0
## sample_TTAGGC_Div4 0 0 0 0 0 0 0
## [,1306] [,1307] [,1308] [,1309] [,1310] [,1311] [,1312]
## sample_ACAAA_Nel3 0 0 0 1 0 0 0
## sample_ACAGTG_Nel5 0 0 0 0 0 0 0
## sample_AGCAT_Nel8 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel10 0 0 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0 0 0
## sample_CGATGT_Nel4 0 0 0 0 0 0 0
## sample_CTAGC_Nel7 0 0 0 0 0 0 0
## sample_CTGTA_Nel12 0 0 0 0 0 0 0
## sample_CTGTA_Nel9 0 0 0 0 0 0 0
## sample_CTTGA_Nel2 0 0 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0 0 0
## sample_TCACC_Nel6 0 0 0 1 0 0 0
## sample_TGACCA_Nel1 0 0 0 0 0 0 0
## sample_AAAAGTT_Alt12 0 0 0 0 0 0 0
## sample_ACAAA_Alt11 0 0 0 0 0 0 0
## sample_ACAGTG_Alt3 0 0 0 0 0 0 0
## sample_AGCCC_Alt13 0 0 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 1 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0 0 0
## sample_CGATGT_Alt1 0 0 0 0 0 0 0
## sample_CTGTA_Alt14 0 0 0 0 0 0 0
## sample_CTTGA_Alt10 0 0 0 0 0 0 0
## sample_GAATTCA_Alt15 0 0 0 0 0 0 0
## sample_GCCAAT_Alt4 0 0 0 0 0 0 0
## sample_GCCAAT_Alt9 0 0 0 0 0 0 0
## sample_TTAGGC_Alt2 0 0 0 0 0 0 0
## sample_TTAGGC_Alt6 0 0 0 0 0 0 0
## sample_TTAGGC_Alt8 0 0 0 0 0 0 0
## sample_AAAAGTT_Sub15 NA NA NA NA NA NA NA
## sample_ACAAA_Sub1 NA 0 0 1 0 0 0
## sample_ACTAT_Sub7 0 0 0 1 0 0 0
## sample_AGCAT_Sub13 0 0 0 0 0 0 0
## sample_AGCCC_Sub11 NA 0 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0 0 0
## sample_CTTGCTT_Sub14 0 NA 0 0 0 0 0
## sample_GAATTCA_Sub9 0 0 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 0
## sample_GTATT_Sub12 0 NA 0 0 NA NA NA
## sample_TGACCA_Sub2 0 0 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 NA NA NA
## sample_ACAGTG_Cau3 0 0 0 0 1 0 0
## sample_ACTAT_Cau11 0 0 0 0 1 0 0
## sample_ACTAT_Cau9 1 NA 0 0 1 0 0
## sample_AGCCC_Cau7 0 0 0 0 1 0 0
## sample_ATGAAAC_Cau12 NA 0 NA NA 1 0 0
## sample_CTAGC_Cau5 0 0 1 0 1 0 0
## sample_CTGTA_Cau8 NA NA 0 0 1 0 0
## sample_GGACCTA_Cau13 NA NA 0 0 1 0 0
## sample_TCACC_Cau1 0 0 0 0 1 0 0
## sample_TCACC_Cau4 0 NA 0 0 NA NA NA
## sample_TGACCA_Cau6 NA 0 0 0 1 0 0
## sample_AAAAGTT_Div12 0 0 0 0 1 0 0
## sample_AAAAGTT_Div13 NA 0 0 0 1 0 0
## sample_ACTAT_Div14 0 1 0 0 1 0 0
## sample_AGCAT_Div11 NA 0 0 0 1 0 0
## sample_AGCCC_Div9 0 0 0 0 1 0 0
## sample_ATCACG_Div1 1 NA 0 0 1 0 0
## sample_ATGAAAC_Div8 0 NA 0 0 1 0 0
## sample_CGATGT_Div3 0 0 0 0 1 0 0
## sample_CTAGC_Div2 1 NA 0 0 1 0 0
## sample_CTTGA_Div6 1 0 0 0 1 0 0
## sample_CTTGCTT_Div15 NA NA 0 0 1 1 1
## sample_GTATT_Div10 NA 0 0 0 1 0 0
## sample_GTATT_Div7 1 0 1 0 1 0 0
## sample_TGACCA_Div5 1 0 0 0 1 0 0
## sample_TTAGGC_Div4 1 0 0 0 1 0 0
## [,1313] [,1314] [,1315] [,1316] [,1317] [,1318] [,1319]
## sample_ACAAA_Nel3 0 0 NA NA 1 0 1
## sample_ACAGTG_Nel5 0 0 0 0 1 0 0
## sample_AGCAT_Nel8 0 1 0 0 1 0 1
## sample_ATGAAAC_Nel10 1 0 NA NA 1 0 1
## sample_ATGAAAC_Nel15 1 0 0 0 0 0 1
## sample_CGATGT_Nel4 0 1 0 0 1 0 1
## sample_CTAGC_Nel7 0 0 0 0 1 0 1
## sample_CTGTA_Nel12 0 1 0 0 0 0 1
## sample_CTGTA_Nel9 0 0 0 0 1 0 1
## sample_CTTGA_Nel2 0 0 0 0 1 0 1
## sample_GGACCTA_Nel11 0 0 0 0 1 0 1
## sample_GGACCTA_Nel13 0 NA 0 0 1 0 1
## sample_GTATT_Nel14 0 0 NA NA 1 0 1
## sample_TCACC_Nel6 0 1 0 0 1 0 1
## sample_TGACCA_Nel1 0 0 0 0 1 0 1
## sample_AAAAGTT_Alt12 0 0 0 0 1 0 0
## sample_ACAAA_Alt11 0 0 0 0 1 0 0
## sample_ACAGTG_Alt3 1 0 0 0 1 0 1
## sample_AGCCC_Alt13 0 0 0 0 1 0 0
## sample_ATCACG_Alt5 0 0 NA NA 0 0 1
## sample_ATCACG_Alt7 0 0 0 0 1 0 0
## sample_CGATGT_Alt1 1 0 0 0 1 0 1
## sample_CTGTA_Alt14 1 1 0 0 1 0 1
## sample_CTTGA_Alt10 1 0 0 0 1 0 1
## sample_GAATTCA_Alt15 1 0 0 0 1 0 0
## sample_GCCAAT_Alt4 0 0 0 0 1 0 1
## sample_GCCAAT_Alt9 1 0 0 0 1 0 1
## sample_TTAGGC_Alt2 0 0 0 0 1 0 1
## sample_TTAGGC_Alt6 1 0 NA NA 1 0 0
## sample_TTAGGC_Alt8 0 0 NA NA 1 0 1
## sample_AAAAGTT_Sub15 0 0 0 0 0 0 NA
## sample_ACAAA_Sub1 0 0 NA NA 0 0 1
## sample_ACTAT_Sub7 0 NA 0 0 0 0 0
## sample_AGCAT_Sub13 0 1 0 0 0 0 1
## sample_AGCCC_Sub11 NA 1 0 0 0 0 NA
## sample_CGATGT_Sub6 0 0 0 0 0 0 1
## sample_CTTGCTT_Sub14 NA 1 NA NA 0 0 0
## sample_GAATTCA_Sub9 0 NA 0 0 0 0 0
## sample_GGACCTA_Sub10 0 0 0 0 0 0 1
## sample_GTATT_Sub12 NA 0 NA NA NA 0 NA
## sample_TGACCA_Sub2 0 0 0 0 0 1 0
## sample_ACAGTG_Cau2 NA 1 NA NA 0 0 0
## sample_ACAGTG_Cau3 0 0 1 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0 0 1
## sample_ACTAT_Cau9 0 0 0 0 0 0 0
## sample_AGCCC_Cau7 0 0 NA NA 0 0 1
## sample_ATGAAAC_Cau12 NA 0 1 0 NA 0 1
## sample_CTAGC_Cau5 0 0 1 0 0 0 0
## sample_CTGTA_Cau8 0 0 NA NA 0 0 NA
## sample_GGACCTA_Cau13 0 1 0 0 0 0 0
## sample_TCACC_Cau1 0 0 1 0 0 0 0
## sample_TCACC_Cau4 NA 0 1 0 NA 0 0
## sample_TGACCA_Cau6 0 1 1 0 0 0 1
## sample_AAAAGTT_Div12 0 0 1 0 0 0 0
## sample_AAAAGTT_Div13 0 1 1 0 0 0 1
## sample_ACTAT_Div14 0 0 0 0 0 0 0
## sample_AGCAT_Div11 NA 0 0 0 NA 0 0
## sample_AGCCC_Div9 0 0 1 0 NA 0 0
## sample_ATCACG_Div1 0 0 1 0 0 0 0
## sample_ATGAAAC_Div8 0 1 0 0 0 0 1
## sample_CGATGT_Div3 0 1 1 1 0 0 0
## sample_CTAGC_Div2 0 1 0 0 0 0 0
## sample_CTTGA_Div6 0 1 1 0 0 0 1
## sample_CTTGCTT_Div15 0 0 1 0 NA 0 0
## sample_GTATT_Div10 0 0 1 0 0 0 1
## sample_GTATT_Div7 0 0 1 0 0 0 0
## sample_TGACCA_Div5 NA 1 1 1 0 0 0
## sample_TTAGGC_Div4 0 0 1 0 0 0 1
## [,1320] [,1321] [,1322] [,1323] [,1324] [,1325] [,1326]
## sample_ACAAA_Nel3 0 0 0 0 1 1 0
## sample_ACAGTG_Nel5 0 0 0 1 0 1 0
## sample_AGCAT_Nel8 0 NA NA NA NA 0 0
## sample_ATGAAAC_Nel10 0 0 0 1 0 1 0
## sample_ATGAAAC_Nel15 0 0 NA NA NA 0 0
## sample_CGATGT_Nel4 0 0 0 1 0 1 0
## sample_CTAGC_Nel7 0 0 NA NA NA 1 0
## sample_CTGTA_Nel12 0 0 0 1 0 NA 0
## sample_CTGTA_Nel9 0 NA 0 1 0 NA 0
## sample_CTTGA_Nel2 0 0 0 0 1 1 0
## sample_GGACCTA_Nel11 0 0 0 0 1 1 0
## sample_GGACCTA_Nel13 0 NA 0 1 0 0 0
## sample_GTATT_Nel14 0 NA 0 1 1 1 0
## sample_TCACC_Nel6 0 NA 0 0 0 1 0
## sample_TGACCA_Nel1 0 0 0 0 0 NA 0
## sample_AAAAGTT_Alt12 0 NA NA NA NA NA NA
## sample_ACAAA_Alt11 0 0 0 1 0 1 0
## sample_ACAGTG_Alt3 0 NA 0 1 0 1 0
## sample_AGCCC_Alt13 0 NA 0 1 0 1 0
## sample_ATCACG_Alt5 0 NA 0 0 0 NA 0
## sample_ATCACG_Alt7 0 NA 0 1 0 1 0
## sample_CGATGT_Alt1 0 0 0 1 0 0 0
## sample_CTGTA_Alt14 0 0 0 1 0 1 0
## sample_CTTGA_Alt10 0 0 0 1 1 1 0
## sample_GAATTCA_Alt15 0 0 0 1 0 1 0
## sample_GCCAAT_Alt4 0 0 NA NA NA 1 0
## sample_GCCAAT_Alt9 0 0 0 1 0 1 0
## sample_TTAGGC_Alt2 0 0 NA NA NA NA 0
## sample_TTAGGC_Alt6 0 0 NA NA NA 1 NA
## sample_TTAGGC_Alt8 0 NA 1 1 0 NA 0
## sample_AAAAGTT_Sub15 NA NA 0 1 0 1 NA
## sample_ACAAA_Sub1 NA 0 0 1 0 1 0
## sample_ACTAT_Sub7 0 0 0 1 0 1 0
## sample_AGCAT_Sub13 0 0 0 1 0 1 0
## sample_AGCCC_Sub11 0 NA 0 1 1 NA NA
## sample_CGATGT_Sub6 NA NA 0 1 0 NA 0
## sample_CTTGCTT_Sub14 NA 0 0 1 0 NA NA
## sample_GAATTCA_Sub9 0 0 0 1 0 1 0
## sample_GGACCTA_Sub10 0 0 0 1 1 0 0
## sample_GTATT_Sub12 0 0 0 1 1 NA NA
## sample_TGACCA_Sub2 0 NA 0 1 1 NA NA
## sample_ACAGTG_Cau2 0 NA 0 1 1 0 0
## sample_ACAGTG_Cau3 NA 0 0 1 0 0 1
## sample_ACTAT_Cau11 0 0 0 1 0 0 0
## sample_ACTAT_Cau9 1 0 0 1 1 0 0
## sample_AGCCC_Cau7 0 0 0 1 1 0 0
## sample_ATGAAAC_Cau12 NA 0 0 1 1 0 0
## sample_CTAGC_Cau5 1 0 0 1 1 0 0
## sample_CTGTA_Cau8 NA NA 0 1 1 0 1
## sample_GGACCTA_Cau13 0 NA 0 1 1 NA 0
## sample_TCACC_Cau1 0 0 0 1 0 0 NA
## sample_TCACC_Cau4 0 0 0 1 0 0 0
## sample_TGACCA_Cau6 1 1 0 1 0 1 0
## sample_AAAAGTT_Div12 0 0 0 1 0 0 0
## sample_AAAAGTT_Div13 0 0 0 1 0 0 0
## sample_ACTAT_Div14 0 0 0 1 1 0 0
## sample_AGCAT_Div11 0 0 0 1 0 0 0
## sample_AGCCC_Div9 1 0 0 1 0 0 0
## sample_ATCACG_Div1 0 0 0 1 1 0 0
## sample_ATGAAAC_Div8 0 0 0 1 0 0 0
## sample_CGATGT_Div3 0 0 NA NA NA 0 0
## sample_CTAGC_Div2 0 0 0 1 0 0 0
## sample_CTTGA_Div6 1 0 0 1 0 0 0
## sample_CTTGCTT_Div15 0 0 0 1 0 0 0
## sample_GTATT_Div10 0 0 0 1 0 0 0
## sample_GTATT_Div7 0 0 0 1 1 0 1
## sample_TGACCA_Div5 1 0 0 1 0 0 0
## sample_TTAGGC_Div4 0 1 1 1 0 0 0
## [,1327] [,1328] [,1329] [,1330] [,1331] [,1332] [,1333]
## sample_ACAAA_Nel3 0 0 1 1 0 1 1
## sample_ACAGTG_Nel5 0 0 1 NA NA NA 1
## sample_AGCAT_Nel8 0 0 1 0 0 1 NA
## sample_ATGAAAC_Nel10 0 0 1 0 0 1 1
## sample_ATGAAAC_Nel15 0 0 1 0 0 1 NA
## sample_CGATGT_Nel4 0 0 1 0 0 1 NA
## sample_CTAGC_Nel7 0 0 1 0 0 1 0
## sample_CTGTA_Nel12 0 0 1 0 0 1 NA
## sample_CTGTA_Nel9 0 0 1 0 1 0 NA
## sample_CTTGA_Nel2 0 0 1 0 0 1 NA
## sample_GGACCTA_Nel11 0 0 1 NA NA NA 1
## sample_GGACCTA_Nel13 0 0 1 0 0 1 1
## sample_GTATT_Nel14 0 0 1 0 0 1 1
## sample_TCACC_Nel6 0 0 1 NA NA NA 1
## sample_TGACCA_Nel1 0 0 1 0 0 1 1
## sample_AAAAGTT_Alt12 NA NA NA NA NA NA NA
## sample_ACAAA_Alt11 0 0 1 0 0 1 1
## sample_ACAGTG_Alt3 0 0 1 0 0 1 1
## sample_AGCCC_Alt13 0 0 1 NA NA NA NA
## sample_ATCACG_Alt5 0 0 1 0 0 1 NA
## sample_ATCACG_Alt7 0 0 1 0 0 1 1
## sample_CGATGT_Alt1 0 0 1 0 0 1 NA
## sample_CTGTA_Alt14 0 0 1 0 0 1 1
## sample_CTTGA_Alt10 0 0 1 0 0 1 1
## sample_GAATTCA_Alt15 0 0 1 0 0 1 NA
## sample_GCCAAT_Alt4 0 0 1 NA NA NA 1
## sample_GCCAAT_Alt9 0 0 1 0 0 1 1
## sample_TTAGGC_Alt2 0 0 1 0 0 1 1
## sample_TTAGGC_Alt6 NA NA NA 0 0 1 NA
## sample_TTAGGC_Alt8 0 0 0 0 0 1 1
## sample_AAAAGTT_Sub15 NA NA NA 0 0 1 NA
## sample_ACAAA_Sub1 0 0 1 0 0 1 0
## sample_ACTAT_Sub7 0 0 1 0 0 1 0
## sample_AGCAT_Sub13 0 0 1 0 0 1 NA
## sample_AGCCC_Sub11 NA NA NA 0 0 1 0
## sample_CGATGT_Sub6 0 0 1 0 0 1 0
## sample_CTTGCTT_Sub14 NA NA NA 0 0 1 NA
## sample_GAATTCA_Sub9 0 0 1 0 0 1 NA
## sample_GGACCTA_Sub10 0 0 1 0 0 1 0
## sample_GTATT_Sub12 NA NA NA 0 0 1 NA
## sample_TGACCA_Sub2 NA NA NA 0 0 1 1
## sample_ACAGTG_Cau2 0 0 1 0 0 1 1
## sample_ACAGTG_Cau3 1 1 1 0 0 1 NA
## sample_ACTAT_Cau11 0 0 0 0 0 1 NA
## sample_ACTAT_Cau9 0 0 0 0 0 1 1
## sample_AGCCC_Cau7 0 0 1 0 0 1 1
## sample_ATGAAAC_Cau12 0 0 0 0 0 1 1
## sample_CTAGC_Cau5 0 0 0 0 0 1 NA
## sample_CTGTA_Cau8 1 1 1 0 0 1 1
## sample_GGACCTA_Cau13 0 0 1 0 0 1 1
## sample_TCACC_Cau1 NA NA NA 0 0 1 1
## sample_TCACC_Cau4 0 0 0 0 0 1 1
## sample_TGACCA_Cau6 0 0 1 0 0 1 1
## sample_AAAAGTT_Div12 0 0 0 0 0 1 1
## sample_AAAAGTT_Div13 0 0 0 0 0 1 1
## sample_ACTAT_Div14 0 0 0 0 0 1 NA
## sample_AGCAT_Div11 0 0 0 0 0 1 0
## sample_AGCCC_Div9 0 0 0 NA NA NA 1
## sample_ATCACG_Div1 0 0 0 0 0 1 NA
## sample_ATGAAAC_Div8 0 0 1 0 0 1 1
## sample_CGATGT_Div3 0 0 0 0 0 1 1
## sample_CTAGC_Div2 0 0 0 0 0 1 NA
## sample_CTTGA_Div6 0 0 0 0 0 1 NA
## sample_CTTGCTT_Div15 0 0 1 0 0 1 1
## sample_GTATT_Div10 0 0 1 0 0 1 NA
## sample_GTATT_Div7 1 1 1 0 0 1 1
## sample_TGACCA_Div5 0 0 0 0 0 1 1
## sample_TTAGGC_Div4 0 0 0 0 0 1 NA
## [,1334] [,1335] [,1336] [,1337] [,1338]
## sample_ACAAA_Nel3 NA NA NA NA NA
## sample_ACAGTG_Nel5 0 0 0 0 0
## sample_AGCAT_Nel8 NA NA NA NA NA
## sample_ATGAAAC_Nel10 0 0 0 0 0
## sample_ATGAAAC_Nel15 0 0 0 0 0
## sample_CGATGT_Nel4 NA NA NA NA NA
## sample_CTAGC_Nel7 0 0 0 0 0
## sample_CTGTA_Nel12 1 0 0 0 0
## sample_CTGTA_Nel9 NA NA NA NA NA
## sample_CTTGA_Nel2 0 0 0 0 0
## sample_GGACCTA_Nel11 0 0 0 0 0
## sample_GGACCTA_Nel13 0 0 0 0 0
## sample_GTATT_Nel14 0 0 0 0 0
## sample_TCACC_Nel6 1 0 0 0 0
## sample_TGACCA_Nel1 NA NA NA NA NA
## sample_AAAAGTT_Alt12 NA NA NA NA NA
## sample_ACAAA_Alt11 0 0 0 0 0
## sample_ACAGTG_Alt3 NA NA NA NA NA
## sample_AGCCC_Alt13 0 0 0 0 0
## sample_ATCACG_Alt5 0 0 0 0 0
## sample_ATCACG_Alt7 0 0 0 0 0
## sample_CGATGT_Alt1 NA NA NA NA NA
## sample_CTGTA_Alt14 NA NA NA NA NA
## sample_CTTGA_Alt10 0 0 0 0 0
## sample_GAATTCA_Alt15 NA NA NA NA NA
## sample_GCCAAT_Alt4 NA NA NA NA NA
## sample_GCCAAT_Alt9 0 0 0 0 0
## sample_TTAGGC_Alt2 NA NA NA NA NA
## sample_TTAGGC_Alt6 0 0 0 0 1
## sample_TTAGGC_Alt8 1 0 0 0 0
## sample_AAAAGTT_Sub15 0 0 0 0 0
## sample_ACAAA_Sub1 NA NA NA NA NA
## sample_ACTAT_Sub7 NA NA NA NA NA
## sample_AGCAT_Sub13 0 0 0 0 0
## sample_AGCCC_Sub11 0 0 0 0 0
## sample_CGATGT_Sub6 0 0 0 0 0
## sample_CTTGCTT_Sub14 1 0 0 0 0
## sample_GAATTCA_Sub9 NA NA NA NA NA
## sample_GGACCTA_Sub10 NA NA NA NA NA
## sample_GTATT_Sub12 0 0 0 0 0
## sample_TGACCA_Sub2 0 0 0 0 0
## sample_ACAGTG_Cau2 0 0 0 0 0
## sample_ACAGTG_Cau3 0 0 0 0 0
## sample_ACTAT_Cau11 0 0 0 0 0
## sample_ACTAT_Cau9 0 0 0 0 0
## sample_AGCCC_Cau7 NA NA NA NA NA
## sample_ATGAAAC_Cau12 0 0 0 0 0
## sample_CTAGC_Cau5 0 0 0 0 0
## sample_CTGTA_Cau8 NA NA NA NA NA
## sample_GGACCTA_Cau13 NA NA NA NA NA
## sample_TCACC_Cau1 NA NA NA NA NA
## sample_TCACC_Cau4 0 0 0 0 0
## sample_TGACCA_Cau6 0 0 1 1 0
## sample_AAAAGTT_Div12 0 0 0 0 0
## sample_AAAAGTT_Div13 0 0 0 0 0
## sample_ACTAT_Div14 NA NA NA NA NA
## sample_AGCAT_Div11 0 0 0 0 0
## sample_AGCCC_Div9 0 0 0 0 0
## sample_ATCACG_Div1 NA NA NA NA NA
## sample_ATGAAAC_Div8 NA NA NA NA NA
## sample_CGATGT_Div3 0 0 0 0 0
## sample_CTAGC_Div2 NA NA NA NA NA
## sample_CTTGA_Div6 0 0 0 0 0
## sample_CTTGCTT_Div15 NA NA NA NA NA
## sample_GTATT_Div10 0 0 0 0 0
## sample_GTATT_Div7 NA NA NA NA NA
## sample_TGACCA_Div5 0 0 0 0 0
## sample_TTAGGC_Div4 0 1 0 0 0Replacing NAs with the Mean
The “for” loop traverses through each column and replaces the NA values with the mean of that specific column. The updated column with the NAs replaces by then mean will take the place of the old column. This is done for every column in the data.
snps_noNAs <- snps_no_invar
N_col <- ncol(snps_no_invar)
for(i in 1:N_col){
# get the current column
column_i <- snps_noNAs[, i]
# get the mean of the current column
mean_i <- mean(column_i, na.rm = TRUE)
# get the NAs in the current column
NAs_i <- which(is.na(column_i))
# record the number of NAs
N_NAs <- length(NAs_i)
# replace the NAs in the current column
column_i[NAs_i] <- mean_i
# replace the original column with the
## updated columns
snps_noNAs[, i] <- column_i
}Save the data
Save the data as a .csv file which can be loaded again later.
write.csv(snps_noNAs, file = "SNPs_cleaned.csv",
row.names = F)Check for the presence of the file with list.files()
list.files(pattern = ".csv")## [1] "SNPs_cleaned.csv" "walsh2017morphology.csv"Next steps:
In Part 2, we will re-load the SNPs_cleaned.csv file and
carry an an analysis with PCA.