Portfolio: Working with VCF files 3: Removing samples with many NAsusing for loops
2022-11-19
Learning objectives
- Review the problem of missing data in SNP datasets
- Introduce the concept of researcher degrees of freedom
- Review how to locate NAs in R using is.na() and which()
- Outline the use of for() loops in R to carry out repetitive tasks.
- Review the use of regular expressions to clean text data.
Introduction
The data we are using to practice working with SNPs in VCF files comes from a paper in Molecular Ecology by Jennifer Walsh called “Subspecies delineation amid phenotypic, geographic and genetic discordance in a songbird.” The goal of the paper is to compare traditional ways of classifying different populations and subspecies of Ammodramus sparrow with morphology and genetic data. In order to do this analysis, though, we need to prepare the data.
Missing data is common in SNP datasets, especially in samples from wild animals where the amount of DNA collected may be small. We can fill in (impute) missing data through methods such as mean imputation. However, if there’s lots of NAs we may want to consider removing samples (in this case birds) for which we’d have to impute many - if not most - of their SNPs. That is to say - if we have to impute a lot of the data for the sample, we’d be better off just removing the sample.
When to remove and when to impute?
There are no strict rules for many of the decisions you have to make when doing data analysis, especially when it comes to preparation and cleaning steps like removing or imputing NAs.
In this study, the authors state:
“we removed any individuals that were missing data at more than 50% of the SNPs.”
This is an arbitrary decision - they could have chosen 60% or 25%. It is therefore called a researcher degree of freedom because they are free to chose what to do, and someone else may have made a different choice.
This type of decision is very common in data analysis, and needs to be documented and justified. Posting the raw data, as the authors have, allows other researchers to explore the consequences of a different choice.
In this exercise we will show how you can remove rows of data if it
is necessary. We’ll use the handy functions which() and
is.na() and a common programming tool called a
for() loop.
Note we are removing individual samples, which are represented by rows in the data. Elsewhere in our protocol we remove columns, for example if all the columns have the same genotype.
Preliminaries
Load the vcfR package 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
## ***** ***** ***** *****Make sure that your working directory is set to the location of the
file all_loci.vcf.
getwd() ## [1] "C:/Users/arhat/Desktop/Computatational Biology"list.files()## [1] "Alggomerative Hierachial Cluster.Rmd"
## [2] "all_loci-1.vcf"
## [3] "all_loci.vcf"
## [4] "bird_snps_remove_NAs.Rmd"
## [5] "code_checkpoint_vcfR.Rmd"
## [6] "my_snp"
## [7] "removing_fixed_alleles.html"
## [8] "removing_fixed_alleles.Rmd"
## [9] "rsconnect"
## [10] "Test.docx"
## [11] "Test.Rmd"
## [12] "transpose_VCF_data.html"
## [13] "transpose_VCF_data.Rmd"
## [14] "vcfR_test.vcf"
## [15] "vcfR_test.vcf.gz"
## [16] "walsh2017morphology.csv"
## [17] "working_directory_practice.html"
## [18] "working_directory_practice.Rmd"list.files(pattern = "vcf")## [1] "all_loci-1.vcf" "all_loci.vcf"
## [3] "code_checkpoint_vcfR.Rmd" "vcfR_test.vcf"
## [5] "vcfR_test.vcf.gz"Data preparation
Load data
Load the all_loci.vcf file into an R data object with
vcfR::read.vcfR().
bird_snps <- vcfR::read.vcfR("all_loci.vcf") ## 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 processedcat("Note - if this didn't work you may not have your working directory set")## Note - if this didn't work you may not have your working directory setGet genotype scores (allele counts)
Use vcfR::extract.gt() to get the genotype scores.
bird_snps_num <- vcfR::extract.gt(bird_snps,
element = "GT",
IDtoRowNames = F,
as.numeric = T,
convertNA = T,
return.alleles = F)Transpose data
Transpose the data with t() so that it has the proper
orientation.
# add t()
bird_snps_num_t <- (bird_snps_num) # TODOConvert the matrix to a dataframe.
# add data.frame()
bird_snps_num_df <- (bird_snps_num_t) # TODORemoving NAs
In order to deal with NAs you must first locate them.
Locating NAs in rows
In this paper, the author’s state that they removed from their analysis data an individual (row) that had missing values (NAs) for >50% of the SNPs. First we need to find them.
NAs can be detected in R using is.na().
Let’s take a look at how many NAs are in the first row of the data.
We’ll use bracket notation of [1, ] to
look at the row.
# Add is.na() and select the first row
## using [1, ]
NAs_row_01 <- is.na(bird_snps_num_t) #TODOis.na() returns a logical vector of
TRUE and FALSE values.
Look at the output of is.na() with
head().
# call head() on the vector NAs_row_01
head(NAs_row_01) # TODO## sample_ACAAA_Nel3 sample_ACAGTG_Nel5 sample_AGCAT_Nel8
## [1,] FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_ATGAAAC_Nel10 sample_ATGAAAC_Nel15 sample_CGATGT_Nel4
## [1,] FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_CTAGC_Nel7 sample_CTGTA_Nel12 sample_CTGTA_Nel9 sample_CTTGA_Nel2
## [1,] FALSE FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE FALSE
## sample_GGACCTA_Nel11 sample_GGACCTA_Nel13 sample_GTATT_Nel14
## [1,] FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_TCACC_Nel6 sample_TGACCA_Nel1 sample_AAAAGTT_Alt12
## [1,] FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_ACAAA_Alt11 sample_ACAGTG_Alt3 sample_AGCCC_Alt13
## [1,] FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_ATCACG_Alt5 sample_ATCACG_Alt7 sample_CGATGT_Alt1
## [1,] FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_CTGTA_Alt14 sample_CTTGA_Alt10 sample_GAATTCA_Alt15
## [1,] FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_GCCAAT_Alt4 sample_GCCAAT_Alt9 sample_TTAGGC_Alt2
## [1,] FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_TTAGGC_Alt6 sample_TTAGGC_Alt8 sample_AAAAGTT_Sub15
## [1,] FALSE FALSE TRUE
## [2,] FALSE FALSE TRUE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_ACAAA_Sub1 sample_ACTAT_Sub7 sample_AGCAT_Sub13 sample_AGCCC_Sub11
## [1,] FALSE FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE TRUE
## [5,] FALSE FALSE FALSE TRUE
## [6,] FALSE FALSE FALSE FALSE
## sample_CGATGT_Sub6 sample_CTAGC_Sub3 sample_CTTGCTT_Sub14
## [1,] TRUE TRUE FALSE
## [2,] TRUE TRUE FALSE
## [3,] FALSE TRUE FALSE
## [4,] FALSE TRUE FALSE
## [5,] FALSE TRUE FALSE
## [6,] FALSE FALSE FALSE
## sample_CTTGCTT_Sub8 sample_GAATTCA_Sub9 sample_GCCAAT_Sub4
## [1,] TRUE FALSE TRUE
## [2,] TRUE FALSE TRUE
## [3,] TRUE FALSE TRUE
## [4,] TRUE FALSE TRUE
## [5,] TRUE FALSE TRUE
## [6,] TRUE FALSE FALSE
## sample_GGACCTA_Sub10 sample_GTATT_Sub12 sample_TGACCA_Sub2
## [1,] FALSE TRUE FALSE
## [2,] FALSE TRUE FALSE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_ACAGTG_Cau2 sample_ACAGTG_Cau3 sample_ACTAT_Cau11 sample_ACTAT_Cau9
## [1,] TRUE FALSE FALSE FALSE
## [2,] TRUE FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE FALSE
## sample_AGCCC_Cau7 sample_ATGAAAC_Cau12 sample_CTAGC_Cau5 sample_CTGTA_Cau8
## [1,] FALSE TRUE FALSE TRUE
## [2,] FALSE TRUE FALSE TRUE
## [3,] FALSE FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE FALSE
## sample_GAATTCA_Cau10 sample_GGACCTA_Cau13 sample_TCACC_Cau1
## [1,] TRUE FALSE FALSE
## [2,] TRUE FALSE FALSE
## [3,] TRUE FALSE FALSE
## [4,] TRUE FALSE FALSE
## [5,] TRUE FALSE FALSE
## [6,] TRUE FALSE FALSE
## sample_TCACC_Cau4 sample_TGACCA_Cau6 sample_AAAAGTT_Div12
## [1,] FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_AAAAGTT_Div13 sample_ACTAT_Div14 sample_AGCAT_Div11
## [1,] FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_AGCCC_Div9 sample_ATCACG_Div1 sample_ATGAAAC_Div8
## [1,] FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_CGATGT_Div3 sample_CTAGC_Div2 sample_CTTGA_Div6
## [1,] FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_CTTGCTT_Div15 sample_GTATT_Div10 sample_GTATT_Div7
## [1,] FALSE FALSE FALSE
## [2,] FALSE FALSE FALSE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE
## [5,] FALSE FALSE FALSE
## [6,] FALSE FALSE FALSE
## sample_TGACCA_Div5 sample_TTAGGC_Div4
## [1,] FALSE FALSE
## [2,] FALSE FALSE
## [3,] FALSE FALSE
## [4,] FALSE FALSE
## [5,] FALSE FALSE
## [6,] FALSE FALSEIn this vector, TRUE means “yes, there was an NA in this position”, and FALSE means “No, no NA there.”
The length of the vector is the length of the entire row we put into
is.na(), meaning we have a TRUE or FALSE answer for every
single value in the row.
We can check this with length() and logical
comparisons.
First, the length of our vector of TRUE/FALSE responses.
# Call length() on NAs_row_01
N_NAs <- length(NAs_row_01) # TODO
N_NAs## [1] 138888Now, the length of our original row
# Call length() on the first row of bird_snps_num_t
## use bracket notation of [1, ] to get the
## first row
length_row <- length(bird_snps_num_t) #TODONow check that they are identical using ==
# Use a logical comparison with ==
## to confirm they are the same length
N_NAs == length_row # TODO## [1] TRUEWe can work directly with a vector of TRUE and
FALSE value, but I find its easiest to first convert this
logical vector into a vector of index
values (indices) that tell us exactly where
the NAs are in the dataframe.
We can get these indices this with which(... == TRUE),
because in the vector TRUE is saying “Yes, its TRUE there
was an NA there.”
# Add which()
which(NAs_row_01 == TRUE) # TODO## [1] 664 665 666 667 668 669 693 744 983 984
## [11] 985 986 987 988 989 990 1158 1159 1470 1471
## [21] 1537 1901 1902 1925 1926 1927 1928 1929 2136 2623
## [31] 2624 3087 3088 3105 3106 3262 3466 3467 3468 3469
## [41] 3470 3471 3472 3473 3848 3849 3850 3853 3873 3989
## [51] 4065 4121 4122 4841 4842 4843 4844 4845 4846 4847
## [61] 4848 5382 5631 5767 5768 5769 5770 5771 5780 5781
## [71] 5782 5783 5784 5785 5786 5787 6076 6372 6373 6604
## [81] 7120 7233 7234 7294 7295 7296 7297 7298 7299 7300
## [91] 7301 7312 7383 7462 7543 7544 7545 7688 7689 7711
## [101] 7895 7896 8081 8379 8503 8504 8505 8533 8691 8692
## [111] 8693 9186 9187 9241 9472 9473 9474 9626 9627 9628
## [121] 9629 9638 9639 9698 9715 9777 10010 10316 10317 10318
## [131] 10319 10320 10321 10389 10528 10529 10652 10653 10654 10655
## [141] 10656 10657 10658 10697 10698 10699 10700 10701 10702 10703
## [151] 10704 10705 10706 10707 10708 10709 10710 10711 11032 11091
## [161] 11092 11182 11183 11184 11185 11186 11187 11188 11189 11221
## [171] 11222 11223 11224 11225 11226 11229 11412 11413 11418 11567
## [181] 11568 11570 11571 11572 11573 11574 11688 11689 11690 11691
## [191] 11692 11951 11952 12267 12318 12626 12627 12628 12629 12630
## [201] 12631 12632 12633 12634 12635 12636 12637 12638 12639 12640
## [211] 12732 12733 12854 12855 12856 12857 12858 12859 12860 12861
## [221] 12862 13044 13045 13111 13112 13113 13114 13115 13116 13117
## [231] 13118 13274 13347 13484 13485 13486 13487 13635 13682 13683
## [241] 14088 14089 14196 14228 14229 14230 14370 14473 14725 14726
## [251] 14746 14783 14784 14785 14786 14787 14788 14789 14790 14791
## [261] 15040 15041 15042 15043 15044 15045 15046 15047 15048 15049
## [271] 15184 15203 15417 15425 15426 15970 16402 16666 16667 16668
## [281] 16669 16670 16671 16672 16673 16674 16766 16767 16768 16769
## [291] 16969 16970 16971 16972 16973 16974 16975 16976 17199 17200
## [301] 17341 17346 17354 17355 17357 17358 17359 17360 17361 17384
## [311] 17385 17386 17387 17388 17414 17755 18086 18087 18088 18105
## [321] 18178 18344 18345 18346 18347 18348 18349 18350 18351 18957
## [331] 19283 19284 19285 19579 19961 19962 19963 19964 19965 19966
## [341] 20173 20174 20260 20273 20274 20275 20276 20277 20278 20279
## [351] 20280 20342 20343 20344 20345 20346 20347 20348 20349 20350
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## [371] 20800 20801 20802 20803 20804 20815 21057 21058 21209 21210
## [381] 21211 21398 21399 21508 22036 22377 22378 22665 22666 22756
## [391] 22757 22758 22759 22760 22761 22762 22763 22992 23117 23118
## [401] 23119 23128 23341 23513 23873 23874 23875 23921 23922 24094
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## [421] 24159 24160 24161 24324 24325 24607 24823 24969 24970 24971
## [431] 24972 24973 24974 24975 24976 24977 24978 24979 24980 25022
## [441] 25023 25049 25050 25057 25185 25186 25187 25188 25189 25190
## [451] 25270 25366 25442 25662 25663 25769 25770 25837 25838 25941
## [461] 26023 26024 26025 26026 26027 26028 26029 26129 26130 26131
## [471] 26132 26133 26134 26135 26136 26137 26138 26139 26140 26141
## [481] 26142 26143 26163 26164 26165 26235 26236 26311 26312 26313
## [491] 26314 26315 26316 26317 26318 26319 26357 26358 26359 26360
## [501] 26361 26362 26363 26364 26365 26602 26614 26615 26616 26617
## [511] 26618 26619 26620 26621 26752 26951 26952 26986 26996 26997
## [521] 26998 27001 27138 27400 27677 27678 27679 27680 27681 27682
## [531] 28026 28027 28028 28029 28030 28031 28032 28033 28058 28059
## [541] 28060 28061 28062 28063 28064 28065 28066 28067 28068 28069
## [551] 28070 28071 28072 28092 28093 28094 28452 28453 28602 28773
## [561] 28774 28920 28931 28932 28933 28934 28935 30844 30845 30846
## [571] 30847 30848 30849 30850 30851 30852 30853 30854 30855 30856
## [581] 30857 30858 30859 30860 30861 30862 30863 30864 30978 30979
## [591] 30980 30981 30982 31057 31514 31542 31543 31544 31545 31624
## [601] 31625 31834 31871 31872 31873 31874 31875 31876 31877 31950
## [611] 31951 31952 31956 32022 32023 32323 32371 32372 32373 32374
## [621] 32375 32376 32377 32378 32539 32709 32710 32711 32738 32739
## [631] 33100 33101 33159 33160 33232 33464 33465 33466 33467 33468
## [641] 33469 33471 33472 33473 33474 33676 33677 33763 34073 34074
## [651] 34075 34076 34077 34078 34079 34080 34081 34132 34702 34718
## [661] 34719 34720 34721 34722 34830 34831 34832 34833 34834 34835
## [671] 34915 34929 35087 35386 35387 35388 35389 35390 35391 35414
## [681] 35466 35482 35483 35511 36002 36003 36004 36005 36006 36007
## [691] 36008 36009 36010 36209 36229 36230 36231 36232 36233 36234
## [701] 36235 36236 36259 36260 36261 36262 36263 36264 36265 36266
## [711] 36422 36543 36544 36545 36546 36547 36548 36549 36550 36551
## [721] 36552 36553 36554 36628 36631 36641 36642 36643 36644 36645
## [731] 36733 36969 36970 36971 36972 36976 36977 37016 37103 37104
## [741] 37105 37106 37107 37108 37109 37110 37140 37383 37395 37396
## [751] 37482 37483 37632 37737 37738 37739 37827 37828 37931 37932
## [761] 37933 37934 37935 37936 37937 37938 37939 38188 38189 38190
## [771] 38191 38192 38193 38194 38195 38325 38424 38516 38552 38553
## [781] 38560 38565 38573 38574 38787 39632 39633 39634 39635 39636
## [791] 39637 39638 39639 39640 39641 39642 39643 39644 39645 39646
## [801] 39698 39699 39700 39701 39702 39703 39704 39711 39756 39757
## [811] 40087 40088 40089 40090 40091 40092 40093 40094 40117 40118
## [821] 40119 40120 40121 40122 40123 40124 40298 40299 40353 40401
## [831] 40402 40403 40404 40405 40406 40407 40408 40409 40410 40411
## [841] 40412 40486 40489 40640 41079 41080 41081 41082 41083 41094
## [851] 41095 41172 41173 41174 41175 41176 41177 41178 41479 41516
## [861] 41517 41518 41519 41520 41521 41522 41685 41686 41743 41744
## [871] 41745 41746 41747 41748 41749 41750 41751 41826 41827 42016
## [881] 42017 42018 42019 42020 42021 42022 42023 42034 42431 42432
## [891] 42434 42435 42436 42437 42438 42552 42553 42554 42555 42556
## [901] 42570 42645 42727 43116 43117 43118 43119 43571 43572 43573
## [911] 43574 43575 43614 43615 43672 43673 43674 43675 43676 43677
## [921] 43678 43679 43680 43963 44112 44259 44260 44261 44262 44263
## [931] 44264 44265 44266 44267 44268 44269 44270 44363 44364 44365
## [941] 44366 44367 44732 45030 45127 45128 45419 45420 45421 45422
## [951] 45423 45424 45425 45426 45427 45428 45429 45430 45431 45432
## [961] 45433 45525 45526 45826 45891 45904 45905 45906 45907 45908
## [971] 45909 45910 45911 46428 46881 46882 46959 47160 47179 47180
## [981] 47266 47303 47304 47305 47306 47307 47308 47309 47348 47349
## [991] 47350 47351 47352 47353 47354 47355 47356 47357 47358 47359
## [1001] 47360 47361 47362 47429 47430 47431 47432 47433 47530 47531
## [1011] 47532 47533 47534 47535 47536 47537 47538 47948 47949 48063
## [1021] 48064 48089 48090 48091 48092 48093 48094 48095 48218 48219
## [1031] 48220 48221 48222 48223 48224 48225 48889 48890 48891 48892
## [1041] 48893 48894 49195 49239 49240 49245 49277 49278 49279 49280
## [1051] 49281 49282 49283 49284 49285 49286 49287 49288 49289 49290
## [1061] 49291 49401 49402 50135 50136 50137 50138 50144 50145 50146
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## [1081] 50791 50832 50833 50834 50835 51206 51207 51208 51209 51210
## [1091] 51211 51212 51213 51214 51215 51216 51217 51218 51219 51220
## [1101] 51240 51241 51242 51330 51331 51661 51662 51663 51664 51665
## [1111] 51666 51667 51668 51679 51701 51829 52098 52668 52669 52747
## [1121] 52748 52749 52750 52751 52752 52922 53553 53554 53993 53994
## [1131] 53995 53996 53997 54008 54009 54010 54011 54012 54597 54598
## [1141] 54683 54684 54685 54686 54687 54688 54690 54691 54692 54693
## [1151] 54982 55019 55020 55021 55022 55023 55024 55025 55081 55082
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## [1171] 55295 55296 55297 55298 55299 55300 55458 55459 55519 55520
## [1181] 55521 55522 55523 55524 55525 55526 55913 55914 55922 55923
## [1191] 55924 55925 55927 55928 55929 55930 55934 55935 56604 56634
## [1201] 56939 56940 56993 56994 56995 56996 56997 56998 56999 57000
## [1211] 57001 57002 57003 57004 57005 57006 57007 57099 57100 57175
## [1221] 57176 57177 57178 57179 57180 57181 57182 57183 57234 57478
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## [1261] 57901 57902 57903 57904 57905 57907 57910 57911 57913 57916
## [1271] 57920 57923 57927 57928 57930 57935 57936 57938 57939 57940
## [1281] 57941 57942 57943 57944 57945 57946 57947 57948 57949 57952
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## [1481] 58327 58328 58329 58332 58333 58334 58335 58336 58337 58338
## [1491] 58339 58340 58341 58342 58346 58347 58354 58355 58356 58357
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## [4281] 70849 70850 70852 70855 70856 70857 70858 70859 70860 70865
## [4291] 70868 70869 70871 70872 70873 70874 70875 70876 70877 70878
## [4301] 70880 70881 70882 70883 70884 70888 70889 70890 70891 70892
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## [4371] 70999 71000 71003 71004 71005 71006 71007 71009 71010 71012
## [4381] 71013 71014 71015 71030 71031 71032 71033 71034 71035 71037
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## [4401] 71053 71054 71055 71056 71057 71058 71059 71060 71061 71062
## [4411] 71063 71064 71065 71066 71067 71069 71071 71072 71073 71074
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## [4431] 71094 71095 71098 71099 71100 71107 71112 71114 71115 71116
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## [4451] 71129 71130 71131 71132 71133 71134 71135 71137 71138 71139
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## [4551] 71284 71285 71286 71294 71295 71296 71299 71300 71301 71302
## [4561] 71303 71304 71305 71306 71307 71308 71309 71314 71315 71316
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## [4601] 71370 71371 71372 71373 71382 71387 71389 71392 71403 71413
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## [4621] 71454 71456 71457 71461 71462 71463 71464 71480 71496 71503
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## [4641] 71565 71579 71582 71590 71592 71593 71599 71600 71601 71602
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## [4671] 71661 71663 71664 71668 71669 71670 71678 71691 71692 71693
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## [4691] 71733 71737 71738 71741 71742 71744 71748 71750 71751 71753
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## [4721] 71836 71837 71842 71843 71849 71855 71858 71859 71861 71865
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## [4751] 71941 71942 71943 71944 71945 71946 71947 71957 71962 71963
## [4761] 71967 71969 71975 71985 71988 71990 71996 71997 71998 72004
## [4771] 72005 72007 72013 72015 72016 72021 72022 72023 72033 72050
## [4781] 72051 72052 72053 72054 72057 72058 72059 72061 72065 72066
## [4791] 72069 72072 72091 72093 72098 72099 72100 72104 72115 72116
## [4801] 72119 72120 72121 72122 72141 72142 72143 72144 72149 72150
## [4811] 72151 72152 72153 72154 72155 72156 72158 72172 72173 72179
## [4821] 72180 72186 72187 72188 72189 72190 72193 72194 72195 72196
## [4831] 72197 72199 72200 72201 72202 72203 72204 72205 72206 72210
## [4841] 72213 72214 72215 72220 72230 72231 72232 72233 72234 72235
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## [4861] 72271 72272 72273 72274 72275 72276 72277 72280 72283 72284
## [4871] 72286 72287 72288 72289 72290 72296 72297 72306 72308 72309
## [4881] 72313 72318 72319 72320 72321 72322 72323 72324 72325 72335
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## [4911] 72391 72392 72393 72394 72395 72396 72397 72398 72399 72400
## [4921] 72410 72411 72414 72457 72458 72459 72460 72461 72466 72468
## [4931] 72469 72482 72483 72485 72490 72491 72492 72493 72494 72495
## [4941] 72496 72497 72498 72499 72500 72503 72506 72507 72508 72509
## [4951] 72510 72516 72517 72518 72531 72532 72534 72535 72536 72537
## [4961] 72539 72544 72545 72547 72548 72555 72556 72557 72560 72561
## [4971] 72562 72563 72566 72569 72570 72571 72574 72575 72584 72592
## [4981] 72601 72602 72603 72606 72624 72625 72626 72637 72652 72662
## [4991] 72663 72668 72669 72681 72682 72685 72686 72687 72689 72696
## [5001] 72697 72700 72701 72702 72707 72708 72709 72710 72721 72724
## [5011] 72728 72729 72730 72731 72737 72738 72742 72743 72744 72745
## [5021] 72746 72754 72755 72756 72757 72759 72764 72765 72766 72767
## [5031] 72768 72769 72772 72775 72776 72779 72784 72794 72795 72796
## [5041] 72797 72801 72802 72807 72819 72820 72821 72822 72826 72827
## [5051] 72832 72833 72834 72837 72843 72844 72846 72850 72852 72856
## [5061] 72857 72874 72876 72877 72908 72910 72911 72912 72913 72914
## [5071] 72915 72916 72917 72918 72919 72921 72922 72930 72931 72935
## [5081] 72936 72938 72939 72942 72943 72944 72959 72960 72961 72962
## [5091] 72963 72964 72970 72971 72972 72973 72974 72975 72978 72980
## [5101] 72981 72982 72991 72995 72996 72998 73003 73007 73009 73010
## [5111] 73035 73041 73047 73048 73049 73055 73066 73067 73070 73073
## [5121] 73075 73081 73082 73086 73087 73089 73090 73096 73097 73109
## [5131] 73114 73115 73120 73121 73126 73133 73137 73138 73139 73146
## [5141] 73147 73148 73149 73152 73153 73154 73155 73156 73157 73162
## [5151] 73165 73173 73174 73190 73191 73192 73193 73194 73195 73196
## [5161] 73197 73198 73199 73200 73201 73202 73203 73204 73205 73207
## [5171] 73213 73214 73223 73225 73228 73231 73232 73233 73234 73235
## [5181] 73236 73237 73238 73243 73244 73245 73246 73247 73248 73252
## [5191] 73257 73263 73270 73274 73275 73279 73281 73287 73288 73289
## [5201] 73290 73291 73295 73296 73303 73304 73305 73306 73307 73308
## [5211] 73309 73310 73311 73312 73313 73314 73315 73316 73317 73318
## [5221] 73319 73320 73321 73322 73323 73324 73325 73326 73327 73328
## [5231] 73329 73330 73331 73332 73333 73334 73335 73336 73337 73338
## [5241] 73339 73340 73341 73342 73343 73344 73345 73346 73347 73348
## [5251] 73349 73350 73351 73352 73353 73354 73355 73356 73357 73358
## [5261] 73359 73360 73361 73362 73363 73364 73365 73366 73367 73368
## [5271] 73369 73370 73371 73372 73373 73374 73375 73376 73377 73378
## [5281] 73379 73380 73381 73382 73383 73384 73385 73386 73387 73388
## [5291] 73389 73390 73391 73392 73393 73394 73395 73396 73397 73398
## [5301] 73399 73400 73401 73402 73403 73404 73405 73406 73407 73408
## [5311] 73409 73410 73411 73412 73413 73414 73415 73416 73417 73418
## [5321] 73419 73420 73421 73422 73423 73424 73425 73426 73427 73428
## [5331] 73429 73430 73431 73432 73433 73434 73435 73436 73437 73438
## [5341] 73439 73440 73441 73442 73443 73444 73445 73446 73447 73448
## [5351] 73449 73450 73451 73452 73453 73454 73455 73456 73457 73458
## [5361] 73459 73460 73461 73462 73463 73464 73465 73466 73467 73468
## [5371] 73469 73470 73471 73472 73473 73474 73475 73476 73477 73478
## [5381] 73479 73480 73481 73482 73483 73484 73485 73486 73487 73488
## [5391] 73489 73490 73491 73492 73493 73494 73495 73496 73497 73498
## [5401] 73499 73500 73501 73502 73503 73504 73505 73506 73507 73508
## [5411] 73510 73511 73512 73513 73514 73515 73516 73517 73518 73519
## [5421] 73520 73521 73522 73523 73524 73525 73526 73527 73528 73529
## [5431] 73530 73531 73532 73533 73534 73535 73536 73537 73538 73539
## [5441] 73540 73541 73542 73543 73544 73545 73546 73547 73548 73549
## [5451] 73550 73551 73552 73553 73554 73555 73556 73557 73558 73559
## [5461] 73560 73561 73562 73563 73564 73565 73566 73567 73568 73569
## [5471] 73570 73571 73572 73573 73574 73575 73576 73577 73578 73579
## [5481] 73580 73581 73582 73583 73584 73585 73586 73587 73588 73589
## [5491] 73590 73591 73592 73593 73594 73595 73596 73597 73598 73599
## [5501] 73600 73601 73606 73607 73608 73609 73610 73611 73612 73613
## [5511] 73614 73615 73616 73617 73618 73619 73620 73621 73622 73623
## [5521] 73626 73627 73628 73629 73630 73631 73632 73633 73634 73635
## [5531] 73636 73637 73638 73639 73640 73641 73642 73643 73644 73645
## [5541] 73646 73647 73648 73649 73650 73651 73652 73653 73654 73655
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## [5561] 73666 73668 73669 73670 73671 73672 73673 73674 73675 73676
## [5571] 73677 73678 73679 73680 73681 73682 73683 73684 73685 73686
## [5581] 73687 73688 73689 73690 73691 73692 73693 73694 73695 73696
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## [5601] 73707 73708 73709 73710 73711 73712 73713 73714 73715 73716
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## [5621] 73727 73728 73729 73730 73731 73732 73733 73734 73735 73736
## [5631] 73737 73738 73739 73740 73741 73742 73743 73744 73745 73746
## [5641] 73747 73748 73749 73750 73751 73752 73753 73754 73755 73756
## [5651] 73757 73758 73759 73760 73761 73762 73763 73764 73765 73766
## [5661] 73767 73768 73769 73770 73771 73772 73773 73774 73775 73776
## [5671] 73777 73778 73779 73780 73781 73782 73783 73784 73785 73786
## [5681] 73787 73788 73789 73790 73791 73792 73793 73794 73795 73796
## [5691] 73797 73798 73799 73800 73801 73802 73803 73804 73805 73806
## [5701] 73807 73808 73809 73810 73811 73812 73813 73814 73815 73816
## [5711] 73817 73818 73819 73820 73821 73822 73823 73824 73825 73826
## [5721] 73827 73828 73829 73830 73831 73832 73833 73834 73835 73836
## [5731] 73837 73838 73839 73840 73841 73842 73843 73844 73845 73846
## [5741] 73847 73848 73849 73850 73851 73852 73853 73854 73855 73856
## [5751] 73857 73858 73859 73860 73861 73862 73863 73864 73865 73866
## [5761] 73867 73868 73869 73870 73871 73872 73873 73874 73875 73876
## [5771] 73877 73878 73879 73880 73881 73882 73883 73884 73885 73886
## [5781] 73889 73890 73891 73892 73893 73894 73895 73896 73897 73898
## [5791] 73899 73900 73901 73902 73903 73904 73905 73906 73907 73908
## [5801] 73909 73910 73911 73912 73913 73914 73915 73916 73917 73918
## [5811] 73919 73920 73921 73922 73923 73924 73925 73926 73927 73928
## [5821] 73929 73930 73931 73932 73933 73934 73935 73936 73938 73939
## [5831] 73941 73942 73943 73944 73945 73946 73947 73948 73949 73950
## [5841] 73951 73952 73953 73954 73955 73956 73957 73958 73959 73960
## [5851] 73961 73962 73963 73964 73965 73966 73967 73968 73969 73970
## [5861] 73971 73972 73973 73974 73975 73976 73977 73978 73979 73980
## [5871] 73981 73982 73983 73984 73985 73986 73987 73988 73989 73990
## [5881] 73991 73992 73993 73994 73995 73996 73997 73998 73999 74000
## [5891] 74001 74002 74003 74004 74005 74006 74007 74008 74009 74010
## [5901] 74011 74012 74013 74014 74015 74016 74017 74018 74019 74020
## [5911] 74021 74022 74023 74024 74025 74026 74027 74028 74029 74030
## [5921] 74031 74032 74033 74034 74035 74036 74037 74038 74039 74040
## [5931] 74041 74042 74043 74044 74045 74047 74048 74049 74050 74051
## [5941] 74052 74053 74054 74055 74056 74057 74058 74059 74060 74061
## [5951] 74064 74065 74066 74067 74068 74069 74070 74071 74072 74073
## [5961] 74074 74075 74076 74077 74078 74079 74080 74081 74082 74083
## [5971] 74084 74085 74086 74087 74088 74089 74090 74091 74092 74093
## [5981] 74094 74095 74096 74097 74098 74099 74100 74101 74102 74103
## [5991] 74104 74105 74106 74107 74108 74109 74110 74111 74112 74113
## [6001] 74114 74115 74116 74117 74118 74119 74120 74121 74122 74123
## [6011] 74124 74125 74126 74127 74128 74129 74130 74131 74132 74133
## [6021] 74134 74135 74136 74137 74138 74139 74140 74141 74142 74143
## [6031] 74144 74145 74146 74147 74148 74149 74150 74151 74152 74153
## [6041] 74154 74155 74156 74157 74158 74159 74160 74161 74162 74163
## [6051] 74164 74165 74166 74167 74168 74169 74170 74171 74172 74173
## [6061] 74174 74175 74176 74177 74178 74179 74180 74181 74182 74183
## [6071] 74184 74185 74186 74187 74188 74189 74190 74191 74192 74193
## [6081] 74194 74195 74196 74197 74198 74199 74200 74201 74202 74203
## [6091] 74204 74205 74206 74207 74208 74209 74210 74211 74212 74213
## [6101] 74214 74215 74216 74217 74218 74219 74220 74221 74222 74223
## [6111] 74224 74225 74226 74227 74228 74229 74230 74231 74232 74233
## [6121] 74234 74235 74236 74237 74238 74239 74240 74241 74242 74243
## [6131] 74244 74245 74246 74247 74248 74249 74250 74251 74252 74253
## [6141] 74254 74255 74256 74257 74258 74259 74260 74261 74262 74263
## [6151] 74264 74265 74266 74267 74268 74269 74270 74271 74273 74274
## [6161] 74275 74276 74280 74281 74282 74283 74284 74285 74286 74287
## [6171] 74288 74289 74290 74291 74292 74293 74294 74295 74296 74297
## [6181] 74298 74299 74300 74301 74302 74303 74304 74305 74306 74307
## [6191] 74308 74309 74310 74311 74312 74313 74314 74315 74316 74317
## [6201] 74318 74319 74320 74321 74322 74323 74324 74325 74326 74327
## [6211] 74328 74329 74330 74331 74332 74333 74334 74335 74336 74337
## [6221] 74338 74339 74340 74341 74342 74343 74344 74345 74346 74347
## [6231] 74348 74349 74350 74351 74352 74353 74354 74355 74356 74357
## [6241] 74358 74359 74360 74361 74362 74363 74364 74365 74366 74367
## [6251] 74368 74369 74370 74371 74372 74373 74374 74375 74376 74377
## [6261] 74378 74379 74380 74381 74382 74383 74384 74385 74386 74387
## [6271] 74388 74389 74390 74391 74392 74393 74394 74395 74396 74397
## [6281] 74398 74399 74400 74401 74402 74403 74404 74405 74406 74407
## [6291] 74408 74409 74410 74411 74412 74413 74414 74415 74416 74417
## [6301] 74418 74419 74420 74421 74422 74423 74424 74425 74426 74427
## [6311] 74428 74429 74430 74431 74432 74433 74434 74435 74436 74437
## [6321] 74438 74439 74440 74441 74442 74443 74444 74445 74446 74447
## [6331] 74448 74449 74450 74451 74452 74453 74454 74455 74456 74457
## [6341] 74458 74459 74460 74461 74462 74463 74464 74465 74466 74467
## [6351] 74468 74469 74470 74471 74472 74473 74474 74475 74476 74477
## [6361] 74478 74479 74480 74481 74482 74483 74484 74485 74486 74487
## [6371] 74488 74489 74490 74491 74492 74493 74494 74495 74496 74497
## [6381] 74498 74499 74500 74501 74502 74503 74504 74505 74506 74507
## [6391] 74508 74509 74510 74511 74512 74513 74514 74515 74516 74517
## [6401] 74518 74519 74520 74521 74522 74523 74524 74525 74526 74527
## [6411] 74528 74529 74530 74531 74532 74533 74534 74535 74536 74537
## [6421] 74538 74539 74540 74541 74542 74543 74544 74545 74546 74547
## [6431] 74548 74549 74550 74551 74552 74553 74554 74555 74556 74557
## [6441] 74558 74559 74560 74561 74562 74563 74564 74565 74566 74567
## [6451] 74568 74569 74570 74571 74572 74573 74574 74575 74576 74577
## [6461] 74578 74579 74580 74581 74582 74583 74584 74585 74586 74587
## [6471] 74588 74589 74590 74591 74592 74593 74594 74595 74596 74597
## [6481] 74598 74599 74600 74601 74602 74603 74604 74605 74606 74607
## [6491] 74608 74609 74610 74611 74612 74613 74614 74615 74616 74617
## [6501] 74618 74619 74620 74621 74622 74623 74624 74625 74626 74627
## [6511] 74628 74629 74630 74631 74632 74633 74634 74635 74636 74637
## [6521] 74638 74639 74640 74642 74643 74644 74645 74646 74647 74648
## [6531] 74649 74650 74651 74652 74653 74654 74655 74656 74657 74658
## [6541] 74659 74660 74661 74662 74663 74664 74665 74666 74667 74668
## [6551] 74669 74670 74671 74672 74673 74674 74675 74676 74677 74678
## [6561] 74679 74680 74681 74682 74683 74684 74685 74686 74687 74688
## [6571] 74689 74690 74691 74692 74693 74694 74695 74696 74697 74698
## [6581] 74699 74700 74701 74702 74703 74704 74705 74706 74707 74708
## [6591] 74709 74710 74711 74712 74713 74714 74715 74716 74717 74718
## [6601] 74719 74720 74721 74722 74723 74724 74725 74726 74727 74728
## [6611] 74729 74730 74731 74732 74733 74734 74735 74736 74737 74738
## [6621] 74739 74740 74741 74742 74743 74744 74745 74746 74747 74748
## [6631] 74749 74750 74751 74752 74753 74754 74755 74756 74757 74758
## [6641] 74759 74760 74761 74762 74763 74764 74765 74766 74767 74768
## [6651] 74770 74771 74772 74773 74774 74775 74776 74777 74778 74779
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## [7301] 77432 77433 77434 77435 77436 77438 77439 77440 77441 77442
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## [7321] 77458 77459 77464 77465 77466 77467 77468 77471 77472 77473
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## [7581] 77834 77835 77836 77837 77838 77839 77840 77841 77842 77843
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## [7681] 77967 77970 77971 77972 77973 77974 77975 77976 77977 77978
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## [7711] 78011 78012 78013 78014 78015 78016 78018 78019 78021 78022
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## [7741] 78056 78057 78058 78059 78060 78061 78062 78063 78064 78065
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## [7831] 78188 78197 78198 78201 78204 78205 78206 78207 78208 78209
## [7841] 78212 78213 78214 78215 78216 78217 78218 78219 78220 78221
## [7851] 78222 78223 78224 78225 78226 78228 78238 78239 78240 78244
## [7861] 78245 78249 78250 78251 78252 78253 78255 78256 78257 78258
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## [7891] 78289 78290 78299 78300 78301 78303 78304 78305 78306 78307
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## [7921] 78333 78334 78335 78336 78337 78339 78340 78341 78342 78343
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## [8181] 78747 78748 78749 78750 78751 78752 78756 78760 78761 78762
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## [8281] 78911 78913 78914 78915 78916 78917 78918 78919 78920 78921
## [8291] 78922 78927 78928 78929 78930 78934 78935 78936 78939 78940
## [8301] 78941 78942 78943 78944 78948 78949 78950 78951 78952 78960
## [8311] 78961 78962 78963 78964 78965 78966 78971 78972 78973 78976
## [8321] 78977 78978 78979 78980 78993 79000 79001 79002 79010 79011
## [8331] 79012 79015 79018 79019 79020 79021 79022 79023 79024 79025
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## [8351] 79049 79050 79051 79052 79053 79057 79058 79059 79060 79061
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## [8381] 79084 79234 79529 79530 79531 79862 79863 80072 80073 80074
## [8391] 80075 80076 80077 80078 80079 80401 80819 80820 80821 81014
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## [8551] 81438 81439 81440 81441 81442 81443 81444 81445 81446 81447
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## [8571] 81488 81501 81503 81504 81506 81510 81511 81514 81523 81524
## [8581] 81528 81530 81531 81532 81537 81539 81543 81548 81552 81556
## [8591] 81557 81558 81559 81560 81561 81563 81564 81568 81569 81570
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## [8641] 81643 81647 81649 81650 81651 81654 81655 81658 81660 81661
## [8651] 81662 81666 81667 81668 81672 81673 81681 81682 81683 81684
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## [8671] 81703 81704 81705 81706 81709 81712 81713 81714 81717 81718
## [8681] 81722 81723 81736 81739 81740 81742 81743 81744 81745 81749
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## [8711] 81831 81838 81839 81840 81841 81842 81844 81845 81846 81847
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## [8751] 81914 81915 81916 81922 81923 81924 81925 81928 81929 81941
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## [8771] 81967 81968 81969 81970 81972 81973 81974 81975 81976 81977
## [8781] 81978 81979 81980 81981 81987 81990 81991 81997 82011 82012
## [8791] 82013 82014 82015 82018 82019 82020 82035 82036 82037 82038
## [8801] 82039 82040 82041 82042 82043 82044 82045 82056 82057 82058
## [8811] 82059 82060 82061 82062 82063 82070 82071 82072 82073 82074
## [8821] 82075 82076 82077 82078 82079 82080 82081 82082 82083 82084
## [8831] 82104 82105 82106 82108 82115 82121 82122 82123 82124 82130
## [8841] 82133 82135 82143 82144 82145 82156 82161 82163 82164 82165
## [8851] 82176 82177 82178 82191 82192 82193 82194 82195 82198 82199
## [8861] 82200 82201 82202 82204 82210 82211 82214 82215 82216 82221
## [8871] 82222 82223 82230 82231 82232 82235 82236 82244 82245 82249
## [8881] 82250 82251 82269 82270 82271 82272 82283 82292 82293 82294
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## [8901] 82318 82323 82326 82327 82328 82329 82331 82332 82338 82339
## [8911] 82345 82346 82347 82352 82353 82354 82355 82357 82366 82367
## [8921] 82369 82371 82377 82378 82379 82380 82381 82383 82384 82385
## [8931] 82386 82387 82388 82389 82397 82404 82406 82407 82408 82409
## [8941] 82415 82416 82417 82420 82421 82422 82423 82424 82426 82429
## [8951] 82430 82431 82434 82440 82441 82443 82445 82451 82452 82455
## [8961] 82456 82458 82463 82464 82465 82471 82472 82475 82476 82477
## [8971] 82478 82479 82483 82484 82497 82498 82499 82500 82506 82507
## [8981] 82508 82511 82512 82515 82516 82517 82518 82519 82520 82536
## [8991] 82537 82538 82539 82542 82546 82547 82553 82554 82563 82564
## [9001] 82566 82567 82574 82580 82581 82583 82584 82586 82589 82604
## [9011] 82605 82606 82607 82608 82609 82614 82618 82619 82620 82621
## [9021] 82622 82624 82627 82630 82631 82637 82640 82641 82646 82648
## [9031] 82652 82654 82655 82656 82657 82658 82659 82663 82668 82672
## [9041] 82673 82674 82680 82681 82682 82686 82688 82689 82690 82691
## [9051] 82693 82694 82703 82704 82705 82706 82709 82711 82712 82713
## [9061] 82714 82723 82724 82725 82726 82727 82734 82735 82736 82737
## [9071] 82741 82753 82754 82757 82758 82761 82765 82766 82769 82778
## [9081] 82782 82783 82784 82794 82797 82798 82799 82804 82805 82809
## [9091] 82810 82818 82819 82820 82821 82822 82823 82832 82833 82834
## [9101] 82837 82838 82839 82840 82841 82842 82843 82844 82845 82846
## [9111] 82847 82848 82849 82850 82860 82868 82869 82870 82872 82873
## [9121] 82876 82877 82878 82879 82880 82881 82882 82883 82892 82893
## [9131] 82902 82903 82904 82905 82908 82909 82912 82913 82914 82915
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## [9161] 83028 83049 83070 83100 83101 83114 83115 83116 83122 83153
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## [9521] 85708 85713 85734 85735 85747 85748 85749 85750 85751 85759
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## [9861] 88443 88461 88521 88522 88528 88541 88556 88559 88560 88574
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## [9931] 89803 89804 89805 89806 89807 89808 89809 89810 89811 89902
## [9941] 89903 89904 90014 90015 90016 90017 90018 90019 90020 90021
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## [10701] 98398 98401 98402 98403 98404 98405 98406 98409 98410 98411
## [10711] 98412 98413 98414 98418 98430 98431 98432 98435 98437 98444
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## [11681] 100713 100714 100715 100716 100717 100718 100719 100720 100721 100722
## [11691] 100723 100724 100725 100726 100727 100728 100729 100730 100731 100732
## [11701] 100733 100734 100735 100736 100737 100738 100739 100740 100741 100742
## [11711] 100743 100744 100745 100746 100747 100748 100749 100750 100751 100752
## [11721] 100753 100754 100755 100756 100757 100758 100759 100760 100761 100762
## [11731] 100763 100764 100765 100766 100767 100768 100769 100770 100771 100772
## [11741] 100773 100774 100775 100776 100777 100778 100779 100780 100781 100782
## [11751] 100783 100784 100785 100786 100787 100788 100789 100790 100791 100792
## [11761] 100793 100794 100795 100796 100797 100798 100799 100800 100801 100802
## [11771] 100803 100804 100805 100806 100807 100808 100809 100810 100811 100812
## [11781] 100813 100814 100815 100816 100817 100818 100819 100820 100821 100822
## [11791] 100823 100824 100825 100826 100827 100828 100829 100830 100831 100832
## [11801] 100833 100834 100835 100836 100837 100838 100839 100840 100841 100842
## [11811] 100843 100844 100845 100846 100847 100848 100849 100850 100851 100852
## [11821] 100853 100854 100855 100856 100857 100858 100859 100860 100861 100862
## [11831] 100863 100864 100865 100866 100867 100868 100869 100870 100871 100872
## [11841] 100873 100874 100875 100876 100877 100878 100879 100880 100881 100882
## [11851] 100883 100884 100885 100886 100887 100888 100889 100890 100891 100892
## [11861] 100895 100896 100897 100898 100899 100900 100901 100902 100903 100904
## [11871] 100905 100906 100907 100908 100909 100910 100911 100912 100913 100914
## [11881] 100915 100916 100917 100918 100919 100920 100921 100922 100923 100924
## [11891] 100925 100926 100927 100928 100929 100930 100931 100932 100933 100934
## [11901] 100935 100936 100937 100938 100939 100940 100941 100942 100943 100944
## [11911] 100945 100946 100947 100948 100949 100950 100951 100952 100953 100954
## [11921] 100955 100956 100957 100958 100959 100960 100961 100962 100963 100964
## [11931] 100965 100966 100967 100968 100969 100970 100971 100972 100973 100974
## [11941] 100975 100976 100977 100979 100980 100981 100982 100983 100984 100985
## [11951] 100986 100987 100988 100989 100990 100991 100992 100993 100994 100995
## [11961] 100996 100997 100998 100999 101000 101001 101002 101003 101004 101005
## [11971] 101006 101007 101008 101009 101010 101011 101012 101013 101014 101015
## [11981] 101016 101017 101018 101019 101020 101021 101022 101023 101024 101025
## [11991] 101026 101027 101028 101029 101030 101031 101032 101033 101034 101035
## [12001] 101036 101037 101038 101039 101041 101042 101043 101044 101045 101046
## [12011] 101047 101048 101049 101050 101051 101053 101054 101055 101056 101057
## [12021] 101058 101059 101060 101061 101062 101063 101064 101065 101066 101067
## [12031] 101068 101069 101070 101076 101077 101078 101079 101080 101081 101082
## [12041] 101083 101084 101085 101086 101087 101088 101089 101090 101091 101092
## [12051] 101093 101094 101095 101096 101097 101098 101099 101100 101101 101102
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## [12071] 101113 101114 101115 101116 101117 101118 101119 101120 101121 101122
## [12081] 101123 101124 101125 101126 101127 101128 101129 101130 101131 101132
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## [12111] 101153 101154 101155 101156 101157 101158 101159 101160 101161 101162
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## [12131] 101173 101174 101175 101176 101177 101178 101179 101180 101181 101182
## [12141] 101183 101184 101185 101186 101187 101188 101189 101190 101191 101192
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## [12171] 101213 101214 101215 101216 101217 101218 101219 101220 101221 101222
## [12181] 101223 101224 101225 101226 101227 101228 101229 101230 101231 101232
## [12191] 101233 101234 101235 101236 101237 101238 101239 101240 101241 101242
## [12201] 101243 101244 101245 101246 101247 101248 101249 101250 101251 101252
## [12211] 101253 101254 101255 101256 101257 101258 101259 101260 101261 101262
## [12221] 101263 101264 101265 101266 101267 101268 101269 101270 101271 101272
## [12231] 101273 101274 101275 101276 101277 101278 101279 101280 101281 101282
## [12241] 101283 101284 101285 101286 101287 101288 101289 101290 101291 101292
## [12251] 101293 101294 101295 101296 101297 101298 101299 101300 101301 101302
## [12261] 101303 101304 101305 101306 101307 101308 101309 101310 101311 101312
## [12271] 101313 101314 101315 101316 101317 101318 101319 101320 101321 101322
## [12281] 101323 101324 101325 101326 101327 101328 101329 101330 101331 101332
## [12291] 101333 101334 101335 101336 101337 101338 101339 101340 101341 101342
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## [12311] 101353 101354 101355 101356 101357 101358 101359 101360 101361 101362
## [12321] 101363 101364 101365 101366 101367 101368 101369 101370 101371 101372
## [12331] 101373 101374 101375 101376 101377 101378 101379 101380 101381 101382
## [12341] 101383 101384 101385 101386 101387 101388 101389 101390 101391 101392
## [12351] 101393 101394 101395 101396 101397 101398 101399 101400 101401 101402
## [12361] 101403 101404 101405 101406 101407 101408 101409 101410 101411 101412
## [12371] 101413 101414 101415 101416 101417 101418 101419 101420 101421 101422
## [12381] 101423 101424 101425 101426 101427 101428 101429 101430 101431 101432
## [12391] 101433 101434 101435 101436 101437 101438 101439 101440 101441 101442
## [12401] 101443 101444 101445 101446 101447 101448 101449 101450 101451 101452
## [12411] 101453 101454 101455 101456 101457 101458 101459 101460 101461 101462
## [12421] 101463 101464 101465 101466 101467 101468 101469 101470 101471 101472
## [12431] 101473 101474 101475 101476 101477 101478 101479 101480 101481 101482
## [12441] 101483 101484 101485 101486 101487 101488 101489 101490 101491 101492
## [12451] 101493 101494 101495 101496 101497 101498 101499 101500 101501 101502
## [12461] 101503 101504 101505 101506 101507 101508 101509 101510 101511 101512
## [12471] 101513 101514 101515 101516 101517 101518 101519 101520 101521 101522
## [12481] 101523 101524 101525 101526 101527 101528 101529 101530 101531 101532
## [12491] 101533 101534 101535 101536 101537 101538 101539 101540 101541 101542
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## [12511] 101553 101554 101555 101556 101557 101558 101559 101560 101561 101562
## [12521] 101563 101564 101565 101566 101567 101568 101569 101570 101571 101572
## [12531] 101573 101574 101575 101576 101577 101578 101579 101580 101581 101582
## [12541] 101583 101584 101585 101586 101587 101588 101589 101590 101591 101592
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## [12561] 101603 101604 101605 101606 101607 101608 101609 101610 101611 101612
## [12571] 101613 101614 101615 101616 101617 101618 101619 101620 101621 101622
## [12581] 101623 101624 101625 101626 101627 101628 101629 101630 101631 101632
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## [12621] 101663 101664 101665 101666 101667 101668 101669 101670 101671 101672
## [12631] 101673 101674 101675 101676 101677 101678 101679 101680 101681 101682
## [12641] 101683 101684 101685 101686 101687 101688 101689 101690 101691 101692
## [12651] 101693 101694 101695 101696 101697 101698 101699 101700 101701 101702
## [12661] 101703 101704 101705 101706 101707 101708 101709 101710 101711 101712
## [12671] 101713 101714 101715 101716 101717 101718 101719 101720 101721 101722
## [12681] 101723 101724 101725 101726 101727 101728 101729 101730 101731 101732
## [12691] 101733 101734 101735 101736 101737 101738 101739 101740 101741 101742
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## [12711] 101753 101754 101755 101756 101757 101758 101759 101760 101761 101762
## [12721] 101763 101764 101765 101766 101767 101768 101769 101770 101771 101772
## [12731] 101773 101774 101776 101777 101778 101779 101780 101781 101782 101783
## [12741] 101784 101785 101786 101787 101788 101789 101790 101791 101792 101793
## [12751] 101794 101795 101796 101797 101798 101799 101800 101801 101802 101803
## [12761] 101804 101805 101806 101807 101808 101809 101810 101811 101812 101813
## [12771] 101814 101815 101816 101817 101818 101819 101820 101821 101822 101823
## [12781] 101824 101825 101826 101827 101828 101829 101830 101831 101832 101833
## [12791] 101834 101835 101836 101837 101843 101844 101845 101846 101847 101848
## [12801] 101849 101850 101851 101852 101853 101854 101855 101856 101857 101858
## [12811] 101859 101860 101861 101862 101863 101864 101865 101866 101867 101868
## [12821] 101869 101870 101871 101872 101873 101874 101875 101876 101877 101878
## [12831] 101879 101880 101881 101882 101883 101884 101885 101886 101887 101888
## [12841] 101889 101890 101891 101892 101893 101894 101895 101896 101897 101898
## [12851] 101899 101901 101902 101903 101904 101905 101906 101907 101908 101909
## [12861] 101910 101911 101912 101913 101914 101915 101916 101917 101918 101919
## [12871] 101920 101921 101922 101923 101924 101925 101926 101927 101928 101929
## [12881] 101930 101931 101932 101933 101934 101935 101936 101937 101938 101939
## [12891] 101940 101941 101942 101943 101944 101945 101946 101947 101948 101949
## [12901] 101950 101951 101952 101953 101954 101955 101956 101957 101958 101959
## [12911] 101960 101961 101962 101963 101964 101965 101966 101967 101968 101969
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## [12931] 101980 101981 101983 101984 101985 101986 101987 101988 101989 101990
## [12941] 101991 101992 101993 101994 101995 101996 101997 101998 101999 102000
## [12951] 102001 102002 102003 102004 102005 102006 102007 102008 102009 102010
## [12961] 102011 102012 102013 102014 102015 102016 102017 102018 102019 102020
## [12971] 102021 102022 102023 102024 102025 102026 102027 102028 102029 102030
## [12981] 102031 102032 102033 102034 102035 102036 102037 102038 102039 102040
## [12991] 102041 102042 102043 102044 102045 102046 102047 102048 102049 102050
## [13001] 102051 102052 102053 102054 102055 102056 102057 102058 102059 102060
## [13011] 102061 102062 102063 102064 102065 102066 102067 102068 102069 102070
## [13021] 102071 102072 102073 102074 102075 102076 102077 102078 102079 102080
## [13031] 102081 102082 102083 102084 102085 102086 102087 102088 102089 102090
## [13041] 102091 102092 102093 102094 102095 102096 102097 102098 102099 102100
## [13051] 102101 102102 102103 102104 102105 102106 102107 102108 102109 102110
## [13061] 102111 102112 102113 102114 102115 102116 102117 102118 102119 102120
## [13071] 102121 102122 102123 102124 102125 102126 102127 102128 102129 102130
## [13081] 102131 102132 102133 102134 102135 102136 102137 102138 102139 102140
## [13091] 102141 102142 102143 102144 102145 102146 102147 102148 102149 102150
## [13101] 102151 102152 102153 102154 102155 102156 102157 102158 102159 102160
## [13111] 102161 102162 102163 102164 102165 102166 102167 102168 102169 102170
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## [13141] 102191 102192 102193 102194 102195 102196 102197 102198 102199 102200
## [13151] 102201 102202 102203 102204 102205 102209 102210 102211 102212 102213
## [13161] 102214 102215 102216 102217 102218 102219 102220 102221 102222 102223
## [13171] 102224 102225 102226 102227 102228 102229 102232 102233 102234 102235
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## [13221] 102592 102603 102604 102617 102627 102631 102637 102638 102639 102645
## [13231] 102703 102704 102713 102725 102729 102734 102735 102736 102737 102743
## [13241] 102765 102766 102778 102779 102787 102788 102789 102790 102791 102849
## [13251] 102852 102872 102876 102877 102885 102886 102893 102897 102915 102916
## [13261] 102917 102918 102923 102930 102931 102932 102983 102984 103010 103011
## [13271] 103018 103020 103023 103027 103028 103036 103037 103095 103096 103102
## [13281] 103103 103126 103127 103128 103129 103130 103131 103132 103133 103134
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## [13311] 103253 103284 103289 103290 103291 103292 103293 103294 103295 103296
## [13321] 103297 103298 103299 103300 103301 103302 103303 103304 103315 103316
## [13331] 103317 103330 103425 103426 103427 103431 103432 103502 103545 103546
## [13341] 103550 103565 103566 103592 103593 103594 103595 103609 103616 103641
## [13351] 103663 103696 103755 103756 103757 103758 103840 103841 103937 103945
## [13361] 103967 103968 103969 103981 103986 103991 103992 103998 104079 104086
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## [13491] 106553 106554 106580 106581 106587 106614 106616 106620 106621 106622
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## [13681] 107918 107919 107920 107921 107922 107923 107924 107925 107926 107927
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## [13721] 109333 109450 109507 109508 109554 109555 109556 109557 109558 109561
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## [13741] 109913 110020 110034 110072 110073 110074 110075 110164 110165 110166
## [13751] 110179 110185 110206 110207 110219 110220 110259 110307 110308 110319
## [13761] 110320 110422 110423 110445 110479 110480 110491 110498 110499 110578
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## [13781] 110811 110812 110818 110907 110908 110909 110910 110911 110912 110913
## [13791] 110914 110936 110937 110938 110939 110940 110941 110942 110943 110960
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## [14021] 114871 114872 114873 114874 114875 114876 114877 114901 114942 114956
## [14031] 115091 115092 115093 115094 115095 115096 115097 115098 115099 115150
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## [14051] 115332 115341 115342 115343 115344 115345 115380 115381 115436 115449
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## [14081] 115821 115831 115847 115859 115860 115861 115862 115863 115871 115902
## [14091] 115903 115905 115906 115923 115924 115925 115926 115927 115929 115930
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## [14131] 116202 116203 116204 116223 116225 116226 116229 116232 116241 116261
## [14141] 116266 116267 116268 116269 116278 116280 116283 116285 116286 116295
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## [14161] 116382 116383 116388 116389 116390 116402 116404 116405 116406 116407
## [14171] 116408 116409 116411 116412 116413 116414 116415 116416 116424 116425
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## [14191] 116514 116522 116553 116566 116567 116571 116572 116598 116599 116612
## [14201] 116613 116614 116615 116647 116671 116672 116673 116686 116687 116688
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## [14221] 116745 116746 116747 116748 116749 116750 116751 116752 116753 116760
## [14231] 116761 116762 116763 116764 116765 116766 116767 116769 116770 116771
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## [14251] 116860 116861 116862 116863 116864 116885 116900 116905 116913 116914
## [14261] 116915 116922 116923 116924 116933 117045 117067 117074 117075 117076
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## [14281] 117167 117185 117197 117198 117219 117233 117234 117264 117275 117277
## [14291] 117278 117279 117280 117281 117282 117283 117284 117285 117286 117309
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## [14321] 117516 117542 117543 117544 117545 117595 117607 117608 117609 117610
## [14331] 117611 117612 117613 117617 117625 117626 117627 117628 117629 117637
## [14341] 117643 117646 117760 117836 117837 117838 117843 118023 118024 118234
## [14351] 118236 118237 118238 118271 118311 118312 118413 118558 118559 118560
## [14361] 118561 118562 118563 118564 118623 118624 118625 118626 118627 118628
## [14371] 118629 118630 118676 118677 118678 118679 118680 118681 118682 118683
## [14381] 118684 118721 118722 118723 118724 118725 118726 118727 118728 118729
## [14391] 118730 118731 118732 118733 118734 118735 118737 118781 118851 118852
## [14401] 118853 118863 118864 118943 118944 118945 118946 118947 118949 118950
## [14411] 118951 118952 118953 118954 118955 118956 118957 119008 119142 119152
## [14421] 119153 119199 119200 119201 119202 119203 119285 119286 119387 119388
## [14431] 119572 119588 119589 119590 119609 119610 119611 119637 119673 119674
## [14441] 119743 119760 119761 119763 119764 119765 119766 119767 119781 119782
## [14451] 119783 119784 119785 119791 119796 119891 119892 119903 119964 119965
## [14461] 120117 120136 120238 120252 120253 120262 120263 120264 120265 120266
## [14471] 120267 120291 120292 120293 120329 120342 120431 120456 120457 120494
## [14481] 120495 120496 120544 120545 120546 120547 120548 120549 120550 120577
## [14491] 120581 120582 120583 120584 120585 120586 120587 120588 120601 120602
## [14501] 120603 120604 120758 120809 120832 120833 120834 120835 120836 120837
## [14511] 120838 120839 120840 120891 120953 120954 120955 120956 121001 121024
## [14521] 121025 121065 121081 121082 121186 121194 121203 121316 121317 121488
## [14531] 121520 121521 121523 121524 121525 121526 121527 121546 121566 121594
## [14541] 121634 121672 121680 121681 121689 121690 121694 121695 121696 121701
## [14551] 121710 121711 121712 121713 121714 121738 121739 121740 121789 121816
## [14561] 121833 121856 121857 121858 121861 121862 121863 121930 121931 121964
## [14571] 121965 121979 121980 121981 121982 121983 121984 121985 121986 122019
## [14581] 122046 122067 122077 122078 122079 122080 122081 122082 122083 122084
## [14591] 122152 122169 122170 122181 122182 122183 122219 122220 122258 122300
## [14601] 122301 122308 122312 122326 122327 122471 122481 122482 122483 122484
## [14611] 122485 122486 122487 122488 122530 122531 122532 122533 122541 122542
## [14621] 122596 122597 122598 122599 122600 122601 122602 122603 122604 122613
## [14631] 122614 122615 122640 122641 122667 122668 122677 122678 122709 122710
## [14641] 122711 122738 122761 122762 122763 122764 122765 122766 122767 122768
## [14651] 122769 122784 122785 122792 122820 122825 122826 122827 122854 122872
## [14661] 122873 122874 122879 122882 122883 122884 122885 122908 122909 122910
## [14671] 122911 122954 122994 123045 123046 123047 123048 123064 123065 123066
## [14681] 123067 123068 123069 123070 123071 123080 123092 123096 123097 123115
## [14691] 123132 123212 123213 123235 123236 123281 123282 123346 123347 123385
## [14701] 123386 123387 123388 123389 123390 123391 123417 123452 123453 123454
## [14711] 123455 123456 123575 123576 123577 123578 123682 123761 124011 124012
## [14721] 124013 124098 124099 124121 124150 124151 124667 124790 124791 124792
## [14731] 124793 124993 124994 124995 124996 124997 124998 124999 125000 125366
## [14741] 125367 125368 125369 125441 125493 125538 125539 125542 125543 125544
## [14751] 125545 125552 125553 125554 125690 125720 125764 125779 126079 126080
## [14761] 126088 126106 126107 126166 126211 126212 126318 126364 126392 126393
## [14771] 126394 126395 126396 126397 126398 126471 126472 126473 126495 126498
## [14781] 126499 126545 126596 126642 126740 126741 126742 126743 126811 126852
## [14791] 126915 126916 126917 126918 126919 126973 126990 127093 127270 127271
## [14801] 127272 127275 127307 127308 127310 127311 127312 127313 127314 127467
## [14811] 127468 127488 127852 127985 127986 127987 127988 127989 127990 128006
## [14821] 128039 128040 128041 128058 128113 128114 128203 128204 128205 128206
## [14831] 128207 128208 128209 128268 128269 128270 128271 128272 128273 128274
## [14841] 128275 128403 128404 128405 128406 128429 128594 128595 128596 128597
## [14851] 128598 128599 128600 128601 128602 128653 129032 129033 129135 129136
## [14861] 129137 129138 129139 129140 129141 129142 129143 129144 129145 129146
## [14871] 129169 129236 129237 129266 129267 129268 129269 129270 129282 129301
## [14881] 129306 129317 129318 129319 129320 129324 129335 129344 129348 129349
## [14891] 129362 129363 129364 129365 129380 129396 129397 129405 129406 129408
## [14901] 129409 129410 129411 129412 129414 129417 129422 129423 129425 129426
## [14911] 129427 129428 129429 129430 129439 129449 129494 129495 129496 129497
## [14921] 129505 129509 129510 129513 129514 129527 129528 129529 129532 129533
## [14931] 129536 129537 129538 129539 129540 129548 129549 129568 129569 129577
## [14941] 129578 129579 129582 129583 129584 129597 129598 129609 129610 129622
## [14951] 129630 129632 129633 129636 129643 129644 129645 129657 129663 129664
## [14961] 129665 129680 129681 129691 129692 129693 129695 129696 129697 129698
## [14971] 129699 129700 129701 129702 129711 129712 129713 129726 129732 129735
## [14981] 129739 129749 129762 129764 129771 129772 129781 129783 129786 129788
## [14991] 129789 129798 129799 129800 129810 129811 129812 129827 129840 129841
## [15001] 129842 129860 129863 129864 129868 129876 129885 129886 129891 129892
## [15011] 129893 129895 129905 129914 129915 129916 129917 129918 129919 129929
## [15021] 129930 129931 129935 129936 129937 129938 129950 129951 129952 129953
## [15031] 129954 129955 129956 129961 129974 129989 129990 130016 130017 130019
## [15041] 130020 130021 130025 130028 130040 130041 130042 130043 130071 130072
## [15051] 130074 130075 130098 130099 130101 130102 130104 130105 130108 130114
## [15061] 130115 130116 130117 130118 130130 130139 130140 130141 130168 130172
## [15071] 130173 130174 130175 130176 130188 130205 130206 130209 130212 130214
## [15081] 130222 130226 130227 130228 130229 130230 130231 130232 130233 130238
## [15091] 130246 130247 130248 130249 130263 130264 130265 130266 130267 130268
## [15101] 130269 130270 130284 130290 130295 130296 130297 130298 130299 130300
## [15111] 130301 130302 130303 130304 130305 130306 130307 130308 130309 130312
## [15121] 130313 130314 130315 130316 130317 130318 130319 130320 130336 130356
## [15131] 130357 130373 130374 130391 130392 130398 130399 130400 130403 130416
## [15141] 130424 130436 130454 130508 130517 130518 130519 130520 130521 130536
## [15151] 130548 130556 130557 130565 130566 130567 130570 130571 130572 130588
## [15161] 130589 130590 130591 130595 130612 130613 130614 130624 130625 130626
## [15171] 130627 130646 130659 130667 130682 130726 130727 130728 130767 130778
## [15181] 130780 130781 130782 130783 130784 130785 130786 130787 130796 130812
## [15191] 130813 130814 130826 130827 130831 130843 130844 130845 130846 130847
## [15201] 130848 130868 130871 130877 130893 130928 130929 130931 130932 130933
## [15211] 130936 130937 130938 130951 130952 130959 130960 130982 130983 130987
## [15221] 130990 130991 130997 130998 131003 131012 131013 131016 131017 131018
## [15231] 131033 131034 131035 131043 131044 131045 131046 131047 131048 131062
## [15241] 131063 131064 131065 131066 131067 131068 131069 131070 131071 131072
## [15251] 131073 131074 131075 131083 131084 131086 131087 131110 131111 131112
## [15261] 131128 131129 131130 131131 131132 131133 131146 131149 131168 131169
## [15271] 131170 131171 131172 131188 131195 131196 131197 131198 131199 131225
## [15281] 131239 131240 131246 131249 131253 131263 131273 131291 131292 131293
## [15291] 131294 131370 131398 131404 131425 131426 131437 131438 131439 131461
## [15301] 131478 131506 131507 131508 131547 131551 131586 131592 131593 131594
## [15311] 131610 131641 131642 131657 131658 131664 131684 131685 131686 131700
## [15321] 131701 131712 131715 131717 131718 131769 131770 131771 131797 131820
## [15331] 131821 131822 131837 131843 131844 131845 131846 131847 131848 131865
## [15341] 131897 131898 131899 131903 131945 131946 131959 131998 131999 132027
## [15351] 132028 132038 132044 132045 132046 132047 132059 132126 132127 132128
## [15361] 132129 132130 132131 132132 132133 132167 132179 132180 132181 132182
## [15371] 132183 132184 132185 132192 132193 132194 132195 132196 132197 132198
## [15381] 132199 132214 132215 132241 132242 132243 132244 132245 132246 132247
## [15391] 132248 132249 132267 132268 132285 132286 132290 132291 132292 132293
## [15401] 132294 132295 132296 132327 132328 132329 132345 132365 132383 132423
## [15411] 132424 132425 132426 132452 132453 132454 132455 132456 132457 132458
## [15421] 132459 132460 132465 132476 132477 132483 132499 132506 132507 132508
## [15431] 132509 132534 132575 132629 132630 132651 132665 132666 132709 132710
## [15441] 132711 132712 132713 132714 132715 132716 132743 132755 132756 132777
## [15451] 132797 132800 132802 132806 132817 132863 132881 132921 132932 132945
## [15461] 132962 133060 133061 133094 133095 133120 133140 133156 133159 133169
## [15471] 133176 133177 133178 133182 133202 133203 133220 133221 133222 133223
## [15481] 133224 133232 133249 133250 133251 133252 133254 133255 133258 133259
## [15491] 133260 133261 133266 133267 133268 133269 133270 133272 133284 133285
## [15501] 133286 133287 133288 133299 133311 133312 133313 133314 133327 133335
## [15511] 133363 133367 133368 133390 133407 133428 133429 133430 133431 133432
## [15521] 133433 133435 133436 133437 133454 133467 133468 133480 133509 133521
## [15531] 133522 133523 133538 133539 133563 133564 133565 133569 133584 133586
## [15541] 133587 133593 133620 133629 133630 133639 133641 133644 133646 133647
## [15551] 133651 133652 133653 133654 133655 133656 133657 133658 133671 133672
## [15561] 133673 133674 133675 133718 133726 133741 133751 133760 133765 133766
## [15571] 133767 133768 133769 133770 133793 133801 133807 133826 133827 133828
## [15581] 133847 133848 133850 133874 133875 133886 133900 133901 133908 133927
## [15591] 133928 133956 133957 134030 134031 134063 134064 134072 134121 134122
## [15601] 134123 134124 134125 134126 134127 134128 134153 134154 134155 134156
## [15611] 134157 134158 134159 134160 134161 134162 134163 134164 134165 134166
## [15621] 134167 134170 134171 134172 134173 134174 134175 134176 134177 134178
## [15631] 134187 134188 134189 134216 134231 134246 134256 134257 134258 134265
## [15641] 134274 134282 134295 134296 134312 134358 134359 134394 134399 134400
## [15651] 134401 134411 134412 134414 134428 134435 134436 134437 134438 134452
## [15661] 134466 134482 134483 134484 134485 134489 134490 134491 134504 134517
## [15671] 134527 134549 134550 134558 134559 134566 134567 134568 134584 134585
## [15681] 134649 134650 134672 134689 134694 134695 134706 134726 134729 134735
## [15691] 134739 134788 134789 134809 134810 134814 134815 134824 134830 134855
## [15701] 134856 134861 134862 134874 134920 134921 134941 134942 134950 134956
## [15711] 134966 135026 135027 135028 135029 135030 135088 135125 135292 135384
## [15721] 135385 135477 135513 135519 135568 135663 135918 136000 136013 136014
## [15731] 136015 136016 136017 136018 136019 136020 136082 136083 136084 136085
## [15741] 136086 136087 136088 136089 136090 136091 136092 136093 136094 136095
## [15751] 136096 136106 136118 136119 136120 136121 136122 136145 136175 136190
## [15761] 136281 136282 136283 136310 136311 136312 136313 136314 136315 136316
## [15771] 136317 136318 136364 136365 136366 136367 136369 136395 136433 136513
## [15781] 136514 136655 136693 136885 136927 137179 137653 137654 137785 137786
## [15791] 137942 137943 137944 137945 137946 137947 137948 137949 138011 138012
## [15801] 138013 138014 138015 138016 138017 138018 138019 138020 138021 138022
## [15811] 138023 138024 138025 138239 138240 138241 138242 138243 138244 138245
## [15821] 138246 138247 138385 138426 138442 138443 138477 138478 138479 138480
## [15831] 138489 138490 138491 138492 138493 138535 138536 138537 138538 138539
## [15841] 138540 138881 138882This gives us an vector of index values. We’ll save the vector for later use.
# Assign the output to an object called
## i_NA_row_01
i_NA_row_01 <- which(NAs_row_01 == TRUE) # TODOWe can confirm that these parts of row 1 of our dataframe contain NAs
using the vector we made i_NA_row_01 and bracket notation.
Let’s look at the rows with NAs in column 1, and also see what’s in rows
2 and 3.
#bird_snps_num_t[c(1:3), i_NA_row_01]A NA-seeking function
Here’s a function that will look for NAs in single column or vector, and tell us the index values.
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)
}Let’s test it on the first row of our data.
# run find_NAs() on the first row of
## bird_snps_num_t, using bracket notation [1,]
find_NAs(bird_snps_num_t) # TODO## Results: 15843 NAs present
## .## [1] 664 665 666 667 668 669 693 744 983 984
## [11] 985 986 987 988 989 990 1158 1159 1470 1471
## [21] 1537 1901 1902 1925 1926 1927 1928 1929 2136 2623
## [31] 2624 3087 3088 3105 3106 3262 3466 3467 3468 3469
## [41] 3470 3471 3472 3473 3848 3849 3850 3853 3873 3989
## [51] 4065 4121 4122 4841 4842 4843 4844 4845 4846 4847
## [61] 4848 5382 5631 5767 5768 5769 5770 5771 5780 5781
## [71] 5782 5783 5784 5785 5786 5787 6076 6372 6373 6604
## [81] 7120 7233 7234 7294 7295 7296 7297 7298 7299 7300
## [91] 7301 7312 7383 7462 7543 7544 7545 7688 7689 7711
## [101] 7895 7896 8081 8379 8503 8504 8505 8533 8691 8692
## [111] 8693 9186 9187 9241 9472 9473 9474 9626 9627 9628
## [121] 9629 9638 9639 9698 9715 9777 10010 10316 10317 10318
## [131] 10319 10320 10321 10389 10528 10529 10652 10653 10654 10655
## [141] 10656 10657 10658 10697 10698 10699 10700 10701 10702 10703
## [151] 10704 10705 10706 10707 10708 10709 10710 10711 11032 11091
## [161] 11092 11182 11183 11184 11185 11186 11187 11188 11189 11221
## [171] 11222 11223 11224 11225 11226 11229 11412 11413 11418 11567
## [181] 11568 11570 11571 11572 11573 11574 11688 11689 11690 11691
## [191] 11692 11951 11952 12267 12318 12626 12627 12628 12629 12630
## [201] 12631 12632 12633 12634 12635 12636 12637 12638 12639 12640
## [211] 12732 12733 12854 12855 12856 12857 12858 12859 12860 12861
## [221] 12862 13044 13045 13111 13112 13113 13114 13115 13116 13117
## [231] 13118 13274 13347 13484 13485 13486 13487 13635 13682 13683
## [241] 14088 14089 14196 14228 14229 14230 14370 14473 14725 14726
## [251] 14746 14783 14784 14785 14786 14787 14788 14789 14790 14791
## [261] 15040 15041 15042 15043 15044 15045 15046 15047 15048 15049
## [271] 15184 15203 15417 15425 15426 15970 16402 16666 16667 16668
## [281] 16669 16670 16671 16672 16673 16674 16766 16767 16768 16769
## [291] 16969 16970 16971 16972 16973 16974 16975 16976 17199 17200
## [301] 17341 17346 17354 17355 17357 17358 17359 17360 17361 17384
## [311] 17385 17386 17387 17388 17414 17755 18086 18087 18088 18105
## [321] 18178 18344 18345 18346 18347 18348 18349 18350 18351 18957
## [331] 19283 19284 19285 19579 19961 19962 19963 19964 19965 19966
## [341] 20173 20174 20260 20273 20274 20275 20276 20277 20278 20279
## [351] 20280 20342 20343 20344 20345 20346 20347 20348 20349 20350
## [361] 20351 20352 20353 20354 20355 20356 20623 20797 20798 20799
## [371] 20800 20801 20802 20803 20804 20815 21057 21058 21209 21210
## [381] 21211 21398 21399 21508 22036 22377 22378 22665 22666 22756
## [391] 22757 22758 22759 22760 22761 22762 22763 22992 23117 23118
## [401] 23119 23128 23341 23513 23873 23874 23875 23921 23922 24094
## [411] 24095 24096 24097 24098 24099 24100 24155 24156 24157 24158
## [421] 24159 24160 24161 24324 24325 24607 24823 24969 24970 24971
## [431] 24972 24973 24974 24975 24976 24977 24978 24979 24980 25022
## [441] 25023 25049 25050 25057 25185 25186 25187 25188 25189 25190
## [451] 25270 25366 25442 25662 25663 25769 25770 25837 25838 25941
## [461] 26023 26024 26025 26026 26027 26028 26029 26129 26130 26131
## [471] 26132 26133 26134 26135 26136 26137 26138 26139 26140 26141
## [481] 26142 26143 26163 26164 26165 26235 26236 26311 26312 26313
## [491] 26314 26315 26316 26317 26318 26319 26357 26358 26359 26360
## [501] 26361 26362 26363 26364 26365 26602 26614 26615 26616 26617
## [511] 26618 26619 26620 26621 26752 26951 26952 26986 26996 26997
## [521] 26998 27001 27138 27400 27677 27678 27679 27680 27681 27682
## [531] 28026 28027 28028 28029 28030 28031 28032 28033 28058 28059
## [541] 28060 28061 28062 28063 28064 28065 28066 28067 28068 28069
## [551] 28070 28071 28072 28092 28093 28094 28452 28453 28602 28773
## [561] 28774 28920 28931 28932 28933 28934 28935 30844 30845 30846
## [571] 30847 30848 30849 30850 30851 30852 30853 30854 30855 30856
## [581] 30857 30858 30859 30860 30861 30862 30863 30864 30978 30979
## [591] 30980 30981 30982 31057 31514 31542 31543 31544 31545 31624
## [601] 31625 31834 31871 31872 31873 31874 31875 31876 31877 31950
## [611] 31951 31952 31956 32022 32023 32323 32371 32372 32373 32374
## [621] 32375 32376 32377 32378 32539 32709 32710 32711 32738 32739
## [631] 33100 33101 33159 33160 33232 33464 33465 33466 33467 33468
## [641] 33469 33471 33472 33473 33474 33676 33677 33763 34073 34074
## [651] 34075 34076 34077 34078 34079 34080 34081 34132 34702 34718
## [661] 34719 34720 34721 34722 34830 34831 34832 34833 34834 34835
## [671] 34915 34929 35087 35386 35387 35388 35389 35390 35391 35414
## [681] 35466 35482 35483 35511 36002 36003 36004 36005 36006 36007
## [691] 36008 36009 36010 36209 36229 36230 36231 36232 36233 36234
## [701] 36235 36236 36259 36260 36261 36262 36263 36264 36265 36266
## [711] 36422 36543 36544 36545 36546 36547 36548 36549 36550 36551
## [721] 36552 36553 36554 36628 36631 36641 36642 36643 36644 36645
## [731] 36733 36969 36970 36971 36972 36976 36977 37016 37103 37104
## [741] 37105 37106 37107 37108 37109 37110 37140 37383 37395 37396
## [751] 37482 37483 37632 37737 37738 37739 37827 37828 37931 37932
## [761] 37933 37934 37935 37936 37937 37938 37939 38188 38189 38190
## [771] 38191 38192 38193 38194 38195 38325 38424 38516 38552 38553
## [781] 38560 38565 38573 38574 38787 39632 39633 39634 39635 39636
## [791] 39637 39638 39639 39640 39641 39642 39643 39644 39645 39646
## [801] 39698 39699 39700 39701 39702 39703 39704 39711 39756 39757
## [811] 40087 40088 40089 40090 40091 40092 40093 40094 40117 40118
## [821] 40119 40120 40121 40122 40123 40124 40298 40299 40353 40401
## [831] 40402 40403 40404 40405 40406 40407 40408 40409 40410 40411
## [841] 40412 40486 40489 40640 41079 41080 41081 41082 41083 41094
## [851] 41095 41172 41173 41174 41175 41176 41177 41178 41479 41516
## [861] 41517 41518 41519 41520 41521 41522 41685 41686 41743 41744
## [871] 41745 41746 41747 41748 41749 41750 41751 41826 41827 42016
## [881] 42017 42018 42019 42020 42021 42022 42023 42034 42431 42432
## [891] 42434 42435 42436 42437 42438 42552 42553 42554 42555 42556
## [901] 42570 42645 42727 43116 43117 43118 43119 43571 43572 43573
## [911] 43574 43575 43614 43615 43672 43673 43674 43675 43676 43677
## [921] 43678 43679 43680 43963 44112 44259 44260 44261 44262 44263
## [931] 44264 44265 44266 44267 44268 44269 44270 44363 44364 44365
## [941] 44366 44367 44732 45030 45127 45128 45419 45420 45421 45422
## [951] 45423 45424 45425 45426 45427 45428 45429 45430 45431 45432
## [961] 45433 45525 45526 45826 45891 45904 45905 45906 45907 45908
## [971] 45909 45910 45911 46428 46881 46882 46959 47160 47179 47180
## [981] 47266 47303 47304 47305 47306 47307 47308 47309 47348 47349
## [991] 47350 47351 47352 47353 47354 47355 47356 47357 47358 47359
## [1001] 47360 47361 47362 47429 47430 47431 47432 47433 47530 47531
## [1011] 47532 47533 47534 47535 47536 47537 47538 47948 47949 48063
## [1021] 48064 48089 48090 48091 48092 48093 48094 48095 48218 48219
## [1031] 48220 48221 48222 48223 48224 48225 48889 48890 48891 48892
## [1041] 48893 48894 49195 49239 49240 49245 49277 49278 49279 49280
## [1051] 49281 49282 49283 49284 49285 49286 49287 49288 49289 49290
## [1061] 49291 49401 49402 50135 50136 50137 50138 50144 50145 50146
## [1071] 50149 50150 50151 50152 50153 50154 50207 50325 50347 50790
## [1081] 50791 50832 50833 50834 50835 51206 51207 51208 51209 51210
## [1091] 51211 51212 51213 51214 51215 51216 51217 51218 51219 51220
## [1101] 51240 51241 51242 51330 51331 51661 51662 51663 51664 51665
## [1111] 51666 51667 51668 51679 51701 51829 52098 52668 52669 52747
## [1121] 52748 52749 52750 52751 52752 52922 53553 53554 53993 53994
## [1131] 53995 53996 53997 54008 54009 54010 54011 54012 54597 54598
## [1141] 54683 54684 54685 54686 54687 54688 54690 54691 54692 54693
## [1151] 54982 55019 55020 55021 55022 55023 55024 55025 55081 55082
## [1161] 55083 55084 55085 55086 55087 55088 55089 55292 55293 55294
## [1171] 55295 55296 55297 55298 55299 55300 55458 55459 55519 55520
## [1181] 55521 55522 55523 55524 55525 55526 55913 55914 55922 55923
## [1191] 55924 55925 55927 55928 55929 55930 55934 55935 56604 56634
## [1201] 56939 56940 56993 56994 56995 56996 56997 56998 56999 57000
## [1211] 57001 57002 57003 57004 57005 57006 57007 57099 57100 57175
## [1221] 57176 57177 57178 57179 57180 57181 57182 57183 57234 57478
## [1231] 57479 57480 57481 57482 57483 57484 57485 57593 57626 57627
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## [4641] 71565 71579 71582 71590 71592 71593 71599 71600 71601 71602
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## [4771] 72005 72007 72013 72015 72016 72021 72022 72023 72033 72050
## [4781] 72051 72052 72053 72054 72057 72058 72059 72061 72065 72066
## [4791] 72069 72072 72091 72093 72098 72099 72100 72104 72115 72116
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## [4871] 72286 72287 72288 72289 72290 72296 72297 72306 72308 72309
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## [4931] 72469 72482 72483 72485 72490 72491 72492 72493 72494 72495
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## [4951] 72510 72516 72517 72518 72531 72532 72534 72535 72536 72537
## [4961] 72539 72544 72545 72547 72548 72555 72556 72557 72560 72561
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## [4981] 72601 72602 72603 72606 72624 72625 72626 72637 72652 72662
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## [5001] 72697 72700 72701 72702 72707 72708 72709 72710 72721 72724
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## [5021] 72746 72754 72755 72756 72757 72759 72764 72765 72766 72767
## [5031] 72768 72769 72772 72775 72776 72779 72784 72794 72795 72796
## [5041] 72797 72801 72802 72807 72819 72820 72821 72822 72826 72827
## [5051] 72832 72833 72834 72837 72843 72844 72846 72850 72852 72856
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## [5091] 72963 72964 72970 72971 72972 72973 72974 72975 72978 72980
## [5101] 72981 72982 72991 72995 72996 72998 73003 73007 73009 73010
## [5111] 73035 73041 73047 73048 73049 73055 73066 73067 73070 73073
## [5121] 73075 73081 73082 73086 73087 73089 73090 73096 73097 73109
## [5131] 73114 73115 73120 73121 73126 73133 73137 73138 73139 73146
## [5141] 73147 73148 73149 73152 73153 73154 73155 73156 73157 73162
## [5151] 73165 73173 73174 73190 73191 73192 73193 73194 73195 73196
## [5161] 73197 73198 73199 73200 73201 73202 73203 73204 73205 73207
## [5171] 73213 73214 73223 73225 73228 73231 73232 73233 73234 73235
## [5181] 73236 73237 73238 73243 73244 73245 73246 73247 73248 73252
## [5191] 73257 73263 73270 73274 73275 73279 73281 73287 73288 73289
## [5201] 73290 73291 73295 73296 73303 73304 73305 73306 73307 73308
## [5211] 73309 73310 73311 73312 73313 73314 73315 73316 73317 73318
## [5221] 73319 73320 73321 73322 73323 73324 73325 73326 73327 73328
## [5231] 73329 73330 73331 73332 73333 73334 73335 73336 73337 73338
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## [5251] 73349 73350 73351 73352 73353 73354 73355 73356 73357 73358
## [5261] 73359 73360 73361 73362 73363 73364 73365 73366 73367 73368
## [5271] 73369 73370 73371 73372 73373 73374 73375 73376 73377 73378
## [5281] 73379 73380 73381 73382 73383 73384 73385 73386 73387 73388
## [5291] 73389 73390 73391 73392 73393 73394 73395 73396 73397 73398
## [5301] 73399 73400 73401 73402 73403 73404 73405 73406 73407 73408
## [5311] 73409 73410 73411 73412 73413 73414 73415 73416 73417 73418
## [5321] 73419 73420 73421 73422 73423 73424 73425 73426 73427 73428
## [5331] 73429 73430 73431 73432 73433 73434 73435 73436 73437 73438
## [5341] 73439 73440 73441 73442 73443 73444 73445 73446 73447 73448
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## [5361] 73459 73460 73461 73462 73463 73464 73465 73466 73467 73468
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## [5391] 73489 73490 73491 73492 73493 73494 73495 73496 73497 73498
## [5401] 73499 73500 73501 73502 73503 73504 73505 73506 73507 73508
## [5411] 73510 73511 73512 73513 73514 73515 73516 73517 73518 73519
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## [5471] 73570 73571 73572 73573 73574 73575 73576 73577 73578 73579
## [5481] 73580 73581 73582 73583 73584 73585 73586 73587 73588 73589
## [5491] 73590 73591 73592 73593 73594 73595 73596 73597 73598 73599
## [5501] 73600 73601 73606 73607 73608 73609 73610 73611 73612 73613
## [5511] 73614 73615 73616 73617 73618 73619 73620 73621 73622 73623
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## [5601] 73707 73708 73709 73710 73711 73712 73713 73714 73715 73716
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## [5691] 73797 73798 73799 73800 73801 73802 73803 73804 73805 73806
## [5701] 73807 73808 73809 73810 73811 73812 73813 73814 73815 73816
## [5711] 73817 73818 73819 73820 73821 73822 73823 73824 73825 73826
## [5721] 73827 73828 73829 73830 73831 73832 73833 73834 73835 73836
## [5731] 73837 73838 73839 73840 73841 73842 73843 73844 73845 73846
## [5741] 73847 73848 73849 73850 73851 73852 73853 73854 73855 73856
## [5751] 73857 73858 73859 73860 73861 73862 73863 73864 73865 73866
## [5761] 73867 73868 73869 73870 73871 73872 73873 73874 73875 73876
## [5771] 73877 73878 73879 73880 73881 73882 73883 73884 73885 73886
## [5781] 73889 73890 73891 73892 73893 73894 73895 73896 73897 73898
## [5791] 73899 73900 73901 73902 73903 73904 73905 73906 73907 73908
## [5801] 73909 73910 73911 73912 73913 73914 73915 73916 73917 73918
## [5811] 73919 73920 73921 73922 73923 73924 73925 73926 73927 73928
## [5821] 73929 73930 73931 73932 73933 73934 73935 73936 73938 73939
## [5831] 73941 73942 73943 73944 73945 73946 73947 73948 73949 73950
## [5841] 73951 73952 73953 73954 73955 73956 73957 73958 73959 73960
## [5851] 73961 73962 73963 73964 73965 73966 73967 73968 73969 73970
## [5861] 73971 73972 73973 73974 73975 73976 73977 73978 73979 73980
## [5871] 73981 73982 73983 73984 73985 73986 73987 73988 73989 73990
## [5881] 73991 73992 73993 73994 73995 73996 73997 73998 73999 74000
## [5891] 74001 74002 74003 74004 74005 74006 74007 74008 74009 74010
## [5901] 74011 74012 74013 74014 74015 74016 74017 74018 74019 74020
## [5911] 74021 74022 74023 74024 74025 74026 74027 74028 74029 74030
## [5921] 74031 74032 74033 74034 74035 74036 74037 74038 74039 74040
## [5931] 74041 74042 74043 74044 74045 74047 74048 74049 74050 74051
## [5941] 74052 74053 74054 74055 74056 74057 74058 74059 74060 74061
## [5951] 74064 74065 74066 74067 74068 74069 74070 74071 74072 74073
## [5961] 74074 74075 74076 74077 74078 74079 74080 74081 74082 74083
## [5971] 74084 74085 74086 74087 74088 74089 74090 74091 74092 74093
## [5981] 74094 74095 74096 74097 74098 74099 74100 74101 74102 74103
## [5991] 74104 74105 74106 74107 74108 74109 74110 74111 74112 74113
## [6001] 74114 74115 74116 74117 74118 74119 74120 74121 74122 74123
## [6011] 74124 74125 74126 74127 74128 74129 74130 74131 74132 74133
## [6021] 74134 74135 74136 74137 74138 74139 74140 74141 74142 74143
## [6031] 74144 74145 74146 74147 74148 74149 74150 74151 74152 74153
## [6041] 74154 74155 74156 74157 74158 74159 74160 74161 74162 74163
## [6051] 74164 74165 74166 74167 74168 74169 74170 74171 74172 74173
## [6061] 74174 74175 74176 74177 74178 74179 74180 74181 74182 74183
## [6071] 74184 74185 74186 74187 74188 74189 74190 74191 74192 74193
## [6081] 74194 74195 74196 74197 74198 74199 74200 74201 74202 74203
## [6091] 74204 74205 74206 74207 74208 74209 74210 74211 74212 74213
## [6101] 74214 74215 74216 74217 74218 74219 74220 74221 74222 74223
## [6111] 74224 74225 74226 74227 74228 74229 74230 74231 74232 74233
## [6121] 74234 74235 74236 74237 74238 74239 74240 74241 74242 74243
## [6131] 74244 74245 74246 74247 74248 74249 74250 74251 74252 74253
## [6141] 74254 74255 74256 74257 74258 74259 74260 74261 74262 74263
## [6151] 74264 74265 74266 74267 74268 74269 74270 74271 74273 74274
## [6161] 74275 74276 74280 74281 74282 74283 74284 74285 74286 74287
## [6171] 74288 74289 74290 74291 74292 74293 74294 74295 74296 74297
## [6181] 74298 74299 74300 74301 74302 74303 74304 74305 74306 74307
## [6191] 74308 74309 74310 74311 74312 74313 74314 74315 74316 74317
## [6201] 74318 74319 74320 74321 74322 74323 74324 74325 74326 74327
## [6211] 74328 74329 74330 74331 74332 74333 74334 74335 74336 74337
## [6221] 74338 74339 74340 74341 74342 74343 74344 74345 74346 74347
## [6231] 74348 74349 74350 74351 74352 74353 74354 74355 74356 74357
## [6241] 74358 74359 74360 74361 74362 74363 74364 74365 74366 74367
## [6251] 74368 74369 74370 74371 74372 74373 74374 74375 74376 74377
## [6261] 74378 74379 74380 74381 74382 74383 74384 74385 74386 74387
## [6271] 74388 74389 74390 74391 74392 74393 74394 74395 74396 74397
## [6281] 74398 74399 74400 74401 74402 74403 74404 74405 74406 74407
## [6291] 74408 74409 74410 74411 74412 74413 74414 74415 74416 74417
## [6301] 74418 74419 74420 74421 74422 74423 74424 74425 74426 74427
## [6311] 74428 74429 74430 74431 74432 74433 74434 74435 74436 74437
## [6321] 74438 74439 74440 74441 74442 74443 74444 74445 74446 74447
## [6331] 74448 74449 74450 74451 74452 74453 74454 74455 74456 74457
## [6341] 74458 74459 74460 74461 74462 74463 74464 74465 74466 74467
## [6351] 74468 74469 74470 74471 74472 74473 74474 74475 74476 74477
## [6361] 74478 74479 74480 74481 74482 74483 74484 74485 74486 74487
## [6371] 74488 74489 74490 74491 74492 74493 74494 74495 74496 74497
## [6381] 74498 74499 74500 74501 74502 74503 74504 74505 74506 74507
## [6391] 74508 74509 74510 74511 74512 74513 74514 74515 74516 74517
## [6401] 74518 74519 74520 74521 74522 74523 74524 74525 74526 74527
## [6411] 74528 74529 74530 74531 74532 74533 74534 74535 74536 74537
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## [8821] 82075 82076 82077 82078 82079 82080 82081 82082 82083 82084
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## [8901] 82318 82323 82326 82327 82328 82329 82331 82332 82338 82339
## [8911] 82345 82346 82347 82352 82353 82354 82355 82357 82366 82367
## [8921] 82369 82371 82377 82378 82379 82380 82381 82383 82384 82385
## [8931] 82386 82387 82388 82389 82397 82404 82406 82407 82408 82409
## [8941] 82415 82416 82417 82420 82421 82422 82423 82424 82426 82429
## [8951] 82430 82431 82434 82440 82441 82443 82445 82451 82452 82455
## [8961] 82456 82458 82463 82464 82465 82471 82472 82475 82476 82477
## [8971] 82478 82479 82483 82484 82497 82498 82499 82500 82506 82507
## [8981] 82508 82511 82512 82515 82516 82517 82518 82519 82520 82536
## [8991] 82537 82538 82539 82542 82546 82547 82553 82554 82563 82564
## [9001] 82566 82567 82574 82580 82581 82583 82584 82586 82589 82604
## [9011] 82605 82606 82607 82608 82609 82614 82618 82619 82620 82621
## [9021] 82622 82624 82627 82630 82631 82637 82640 82641 82646 82648
## [9031] 82652 82654 82655 82656 82657 82658 82659 82663 82668 82672
## [9041] 82673 82674 82680 82681 82682 82686 82688 82689 82690 82691
## [9051] 82693 82694 82703 82704 82705 82706 82709 82711 82712 82713
## [9061] 82714 82723 82724 82725 82726 82727 82734 82735 82736 82737
## [9071] 82741 82753 82754 82757 82758 82761 82765 82766 82769 82778
## [9081] 82782 82783 82784 82794 82797 82798 82799 82804 82805 82809
## [9091] 82810 82818 82819 82820 82821 82822 82823 82832 82833 82834
## [9101] 82837 82838 82839 82840 82841 82842 82843 82844 82845 82846
## [9111] 82847 82848 82849 82850 82860 82868 82869 82870 82872 82873
## [9121] 82876 82877 82878 82879 82880 82881 82882 82883 82892 82893
## [9131] 82902 82903 82904 82905 82908 82909 82912 82913 82914 82915
## [9141] 82919 82920 82921 82923 82924 82925 82932 82933 82934 82935
## [9151] 82936 82940 82941 82942 82996 83000 83012 83013 83022 83023
## [9161] 83028 83049 83070 83100 83101 83114 83115 83116 83122 83153
## [9171] 83174 83175 83176 83179 83183 83184 83185 83213 83214 83216
## [9181] 83236 83253 83264 83313 83314 83326 83337 83345 83346 83370
## [9191] 83371 83372 83429 83468 83475 83476 83488 83489 83538 83559
## [9201] 83583 83584 83589 83590 83595 83596 83597 83613 83615 83624
## [9211] 83640 83667 83695 83722 83767 83768 83769 83770 83771 83773
## [9221] 83774 83781 83782 83784 83830 83831 83843 83844 83845 83846
## [9231] 83847 83848 83849 83850 83890 83893 83894 83895 83896 83897
## [9241] 83898 83899 83911 83912 83916 83954 83955 83956 83957 83958
## [9251] 83959 83960 83999 84000 84001 84002 84003 84004 84005 84006
## [9261] 84007 84008 84009 84010 84011 84012 84013 84031 84032 84040
## [9271] 84056 84059 84093 84094 84107 84118 84119 84143 84144 84145
## [9281] 84221 84222 84223 84224 84225 84286 84319 84368 84371 84375
## [9291] 84376 84380 84387 84404 84405 84411 84426 84445 84446 84447
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## [9311] 84552 84556 84609 84632 84633 84648 84671 84726 84727 84728
## [9321] 84737 84749 84750 84751 84752 84789 84853 84856 84861 84862
## [9331] 84863 84864 84865 84877 84878 84892 84894 84897 84904 84915
## [9341] 84927 84928 84931 84932 84934 84935 84939 84943 84944 84951
## [9351] 84952 84953 84957 84967 84983 84995 84996 84997 84998 84999
## [9361] 85006 85013 85014 85019 85022 85028 85038 85039 85043 85044
## [9371] 85045 85057 85059 85060 85061 85062 85063 85065 85066 85070
## [9381] 85071 85072 85095 85096 85102 85108 85109 85112 85113 85114
## [9391] 85138 85141 85142 85143 85145 85154 85155 85156 85165 85169
## [9401] 85170 85171 85172 85173 85180 85182 85200 85210 85211 85212
## [9411] 85215 85216 85230 85231 85234 85236 85240 85242 85243 85251
## [9421] 85255 85264 85279 85280 85290 85313 85323 85324 85325 85326
## [9431] 85327 85338 85339 85340 85345 85346 85347 85359 85361 85362
## [9441] 85368 85372 85388 85389 85390 85397 85401 85410 85416 85421
## [9451] 85422 85426 85427 85428 85429 85430 85441 85443 85444 85445
## [9461] 85451 85452 85467 85478 85493 85495 85501 85504 85509 85510
## [9471] 85512 85513 85516 85518 85519 85524 85525 85526 85532 85539
## [9481] 85540 85541 85542 85543 85544 85545 85547 85548 85549 85550
## [9491] 85551 85552 85560 85561 85570 85571 85572 85601 85602 85603
## [9501] 85607 85621 85624 85633 85639 85640 85641 85642 85643 85649
## [9511] 85650 85669 85670 85671 85675 85676 85689 85702 85703 85707
## [9521] 85708 85713 85734 85735 85747 85748 85749 85750 85751 85759
## [9531] 85760 85761 85762 85783 85805 85806 85807 85808 85816 85819
## [9541] 85820 85840 85841 85842 85845 85847 85855 85871 85879 85880
## [9551] 85881 85882 85883 85884 85885 85886 85887 85888 85889 85896
## [9561] 85897 85898 85899 85900 85901 85902 85903 85905 85906 85907
## [9571] 85908 85918 85919 85957 85958 85962 85963 85964 85965 85967
## [9581] 85988 85989 85990 85991 85993 86021 86022 86023 86026 86027
## [9591] 86028 86029 86030 86047 86048 86049 86050 86051 86052 86053
## [9601] 86057 86060 86061 86087 86089 86090 86098 86099 86109 86127
## [9611] 86128 86129 86133 86134 86141 86150 86151 86152 86153 86154
## [9621] 86169 86180 86181 86186 86187 86189 86191 86203 86210 86211
## [9631] 86212 86213 86215 86227 86229 86241 86242 86243 86244 86245
## [9641] 86246 86247 86257 86258 86259 86260 86270 86271 86272 86273
## [9651] 86274 86275 86279 86300 86302 86304 86305 86310 86315 86316
## [9661] 86329 86330 86333 86334 86335 86355 86369 86370 86377 86391
## [9671] 86394 86395 86396 86397 86399 86411 86413 86414 86415 86416
## [9681] 86417 86418 86419 86420 86421 86422 86429 86438 86439 86444
## [9691] 86445 86446 86447 86462 86463 86464 86465 86466 86467 86481
## [9701] 86506 86510 86512 86513 86533 86534 86535 86536 86537 86552
## [9711] 86564 86565 86566 86567 86569 86570 86578 86585 86592 86593
## [9721] 86594 86595 86612 86617 86618 86623 86624 86636 86637 86643
## [9731] 86644 86652 86667 86668 86676 86677 86678 86679 86680 86681
## [9741] 86682 86695 86696 86719 86720 86728 86731 86741 86742 86746
## [9751] 86747 86748 86749 86760 86761 86762 86763 86770 86771 86772
## [9761] 86773 86777 86778 86782 86785 86800 86827 86860 86863 86872
## [9771] 86897 86906 86913 86914 86915 86916 86917 86918 86962 86963
## [9781] 86964 86965 86970 86971 86979 86998 87067 87070 87100 87101
## [9791] 87102 87144 87145 87159 87160 87199 87244 87288 87346 87347
## [9801] 87369 87375 87376 87377 87378 87379 87456 87497 87501 87536
## [9811] 87537 87551 87552 87554 87602 87603 87631 87632 87642 87671
## [9821] 87775 87784 87846 87847 87848 87900 87901 87910 87911 87915
## [9831] 87920 87943 87950 87969 88113 88114 88139 88140 88141 88142
## [9841] 88170 88174 88175 88176 88193 88194 88195 88208 88253 88254
## [9851] 88270 88271 88278 88323 88324 88325 88326 88391 88392 88430
## [9861] 88443 88461 88521 88522 88528 88541 88556 88559 88560 88574
## [9871] 88575 88578 88597 88626 88627 88628 88629 88630 88631 88632
## [9881] 88633 88634 88635 88636 88637 88660 88696 88713 88728 88808
## [9891] 88945 88946 88947 88995 89068 89069 89070 89272 89478 89680
## [9901] 89681 89682 89683 89684 89685 89686 89704 89717 89718 89719
## [9911] 89720 89721 89722 89723 89724 89786 89787 89788 89789 89790
## [9921] 89791 89792 89793 89794 89795 89796 89797 89798 89799 89800
## [9931] 89803 89804 89805 89806 89807 89808 89809 89810 89811 89902
## [9941] 89903 89904 90014 90015 90016 90017 90018 90019 90020 90021
## [9951] 90022 90566 90656 90657 90830 90831 90832 90837 90925 91288
## [9961] 91311 91312 91314 91407 91462 91463 91500 91521 91522 91550
## [9971] 91646 91647 91648 91649 91650 91651 91652 91653 91715 91716
## [9981] 91717 91718 91719 91720 91721 91722 91723 91724 91725 91726
## [9991] 91727 91728 91729 91754 92193 92194 92195 92196 92197 92372
## [10001] 92402 92403 92553 92614 92631 92639 92640 92696 92700 92701
## [10011] 92702 92703 92704 92705 92716 92717 92718 92719 92737 92759
## [10021] 92760 92761 92763 92764 92765 92766 92771 92772 92788 92812
## [10031] 92816 92817 92825 92826 92843 92844 92853 92916 92931 92948
## [10041] 92949 92995 92996 93068 93079 93081 93122 93130 93181 93182
## [10051] 93185 93214 93215 93216 93220 93234 93235 93246 93247 93270
## [10061] 93271 93272 93273 93279 93286 93287 93299 93300 93301 93302
## [10071] 93303 93304 93305 93378 93385 93386 93387 93418 93419 93420
## [10081] 93421 93424 93425 93457 93488 93489 93490 93517 93565 93571
## [10091] 93574 93606 93607 93608 93634 93635 93678 93679 93680 93702
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## [10111] 93794 93816 93817 93826 93827 93828 93829 93830 93831 93832
## [10121] 93833 93834 93866 93867 93868 93869 93870 93871 93883 93900
## [10131] 93901 93932 93944 93947 93948 93949 93950 93956 93958 93959
## [10141] 93960 93971 93980 93981 93982 94065 94075 94076 94077 94095
## [10151] 94116 94122 94123 94124 94125 94126 94127 94140 94141 94161
## [10161] 94162 94167 94206 94208 94209 94221 94293 94315 94336 94361
## [10171] 94362 94366 94367 94411 94412 94450 94451 94452 94453 94454
## [10181] 94455 94456 94465 94476 94477 94478 94479 94483 94493 94494
## [10191] 94517 94518 94519 94520 94521 94522 94523 94540 94541 94543
## [10201] 94544 94545 94546 94547 94548 94555 94556 94560 94561 94572
## [10211] 94573 94574 94595 94596 94597 94602 94604 94605 94612 94613
## [10221] 94628 94640 94641 94642 94643 94644 94664 94673 94674 94675
## [10231] 94683 94684 94686 94687 94700 94701 94703 94704 94705 94706
## [10241] 94707 94708 94710 94711 94717 94723 94724 94727 94745 94746
## [10251] 94753 94774 94775 94782 94787 94788 94791 94792 94810 94816
## [10261] 94817 94818 94837 94853 94855 94856 94857 94860 94861 94862
## [10271] 94875 94876 94877 94878 94881 94886 94898 94899 94900 94905
## [10281] 94908 94910 94911 94915 94924 94925 94936 94973 94974 94975
## [10291] 94976 94977 94978 94979 94980 94983 94984 94985 94997 95013
## [10301] 95014 95027 95042 95059 95061 95068 95069 95076 95077 95078
## [10311] 95085 95086 95108 95109 95138 95141 95142 95154 95155 95156
## [10321] 95161 95169 95170 95171 95175 95176 95184 95186 95199 95200
## [10331] 95201 95202 95214 95215 95216 95217 95220 95228 95229 95230
## [10341] 95231 95242 95243 95246 95247 95248 95252 95267 95268 95269
## [10351] 95270 95289 95290 95291 95292 95293 95297 95298 95299 95302
## [10361] 95313 95318 95319 95320 95321 95327 95331 95332 95349 95350
## [10371] 95352 95353 95358 95359 95361 95362 95363 95381 95386 95388
## [10381] 95409 95417 95418 95419 95425 95428 95430 95448 95454 95456
## [10391] 95457 95464 95475 95476 95477 95478 95479 95480 95481 95482
## [10401] 95485 95486 95490 95493 95500 95502 95516 95524 95525 95526
## [10411] 95527 95528 95529 95530 95531 95532 95533 95534 95562 95573
## [10421] 95574 95575 95576 95577 95578 95579 95580 95581 95582 95583
## [10431] 95584 95585 95586 95587 95590 95591 95592 95593 95594 95595
## [10441] 95596 95597 95598 95614 95626 95627 95631 95633 95638 95654
## [10451] 95655 95656 95657 95658 95666 95673 95674 95675 95679 95680
## [10461] 95689 95690 95691 95706 95715 95716 95722 95723 95732 95772
## [10471] 95773 95774 95776 95777 95778 95779 95786 95812 95813 95816
## [10481] 95817 95818 95819 95820 95821 95825 95849 95850 95855 95856
## [10491] 95857 95858 95862 95863 95866 95867 95868 95869 95872 95875
## [10501] 95884 95885 95886 95890 95891 95892 95893 95900 95908 95909
## [10511] 95910 95911 95920 95923 95937 95945 95955 95960 95966 95969
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## [10531] 96005 96019 96020 96021 96047 96049 96050 96056 96057 96058
## [10541] 96059 96060 96061 96062 96063 96064 96065 96066 96067 96069
## [10551] 96070 96087 96092 96096 96107 96108 96109 96124 96125 96128
## [10561] 96129 96146 96155 96157 96158 96167 96168 96196 96197 96203
## [10571] 96206 96207 96229 96230 96244 96265 96268 96269 96270 96272
## [10581] 96275 96276 96281 96282 96295 96296 96303 96304 96305 96313
## [10591] 96321 96322 96323 96324 96325 96326 96340 96341 96361 96362
## [10601] 96363 96372 96373 96376 96379 96380 96381 96382 96383 96384
## [10611] 96385 96391 96392 96393 96394 96398 96400 96401 96402 96405
## [10621] 96409 96410 96413 96414 96418 96424 96427 96429 96460 96558
## [10631] 96559 96560 96561 96562 96563 96624 96837 96918 96935 96936
## [10641] 97121 97122 97123 97124 97125 97126 97127 97134 97135 97143
## [10651] 97175 97176 97177 97210 97211 97393 97425 97426 97427 97492
## [10661] 97493 97502 97503 97504 97505 97506 97507 97508 97509 97510
## [10671] 97511 97512 97513 97514 97515 97516 97644 97645 97684 97685
## [10681] 97690 97887 97888 97985 97987 97988 97989 97990 97991 97992
## [10691] 97993 97994 98372 98373 98380 98381 98390 98391 98392 98396
## [10701] 98398 98401 98402 98403 98404 98405 98406 98409 98410 98411
## [10711] 98412 98413 98414 98418 98430 98431 98432 98435 98437 98444
## [10721] 98445 98446 98449 98452 98453 98454 98455 98456 98461 98481
## [10731] 98484 98485 98486 98498 98499 98500 98501 98502 98503 98507
## [10741] 98508 98511 98524 98536 98537 98538 98539 98541 98542 98544
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## [10761] 98565 98566 98570 98571 98572 98575 98580 98584 98589 98593
## [10771] 98603 98604 98605 98606 98607 98608 98613 98618 98619 98620
## [10781] 98621 98622 98630 98631 98632 98633 98640 98641 98645 98646
## [10791] 98649 98650 98657 98658 98659 98672 98673 98674 98675 98676
## [10801] 98677 98684 98685 98691 98692 98693 98694 98704 98705 98716
## [10811] 98717 98718 98719 98720 98725 98726 98745 98746 98747 98748
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## [10861] 98931 98932 98933 98949 98950 98951 98952 98953 98966 98967
## [10871] 98970 98972 98994 98996 99002 99003 99004 99013 99018 99019
## [10881] 99021 99022 99023 99027 99028 99029 99033 99034 99035 99039
## [10891] 99043 99044 99045 99046 99047 99048 99057 99058 99059 99060
## [10901] 99065 99067 99071 99072 99076 99077 99078 99079 99085 99086
## [10911] 99087 99088 99089 99090 99091 99092 99100 99101 99125 99126
## [10921] 99128 99136 99137 99138 99152 99153 99155 99156 99157 99160
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## [10941] 99197 99198 99205 99206 99207 99208 99210 99211 99234 99235
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## [10961] 99271 99272 99273 99274 99275 99276 99277 99278 99279 99280
## [10971] 99281 99282 99283 99304 99308 99309 99312 99317 99318 99324
## [10981] 99351 99358 99360 99361 99362 99363 99364 99365 99366 99367
## [10991] 99368 99369 99370 99371 99382 99383 99384 99385 99393 99394
## [11001] 99395 99416 99420 99421 99422 99423 99424 99426 99429 99446
## [11011] 99447 99460 99461 99465 99466 99467 99472 99474 99475 99482
## [11021] 99484 99485 99489 99491 99492 99493 99494 99507 99508 99517
## [11031] 99519 99520 99523 99524 99534 99535 99536 99537 99538 99540
## [11041] 99541 99542 99543 99545 99558 99560 99561 99562 99563 99564
## [11051] 99566 99567 99568 99569 99570 99580 99581 99592 99593 99598
## [11061] 99608 99609 99630 99631 99632 99636 99637 99644 99653 99654
## [11071] 99655 99656 99657 99658 99670 99672 99676 99677 99678 99679
## [11081] 99683 99687 99688 99689 99694 99699 99700 99713 99714 99715
## [11091] 99716 99720 99721 99724 99725 99726 99727 99731 99733 99734
## [11101] 99735 99736 99737 99738 99739 99740 99742 99744 99745 99746
## [11111] 99747 99751 99752 99758 99765 99766 99767 99768 99769 99776
## [11121] 99777 99781 99782 99783 99787 99790 99795 99803 99813 99816
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## [11141] 99840 99843 99844 99845 99846 99852 99856 99862 99863 99897
## [11151] 99898 99899 99900 99903 99905 99907 99908 99915 99927 99928
## [11161] 99929 99930 99931 99932 99944 99945 99950 99965 99966 99967
## [11171] 99971 99972 99973 99979 99980 99981 99982 99983 99984 99985
## [11181] 99986 99987 99993 99995 99996 99998 100004 100007 100017 100018
## [11191] 100020 100029 100030 100031 100032 100033 100034 100041 100044 100045
## [11201] 100046 100051 100052 100058 100059 100061 100064 100065 100067 100074
## [11211] 100077 100078 100079 100087 100088 100092 100093 100095 100096 100102
## [11221] 100105 100106 100107 100108 100115 100117 100123 100124 100125 100126
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## [11241] 100154 100161 100162 100163 100170 100198 100199 100200 100201 100202
## [11251] 100203 100204 100205 100206 100207 100208 100209 100210 100211 100221
## [11261] 100234 100237 100238 100239 100240 100241 100242 100243 100244 100245
## [11271] 100249 100250 100251 100252 100256 100258 100263 100267 100268 100269
## [11281] 100270 100280 100281 100286 100287 100288 100304 100305 100306 100307
## [11291] 100308 100309 100310 100311 100312 100313 100314 100315 100316 100317
## [11301] 100318 100319 100320 100321 100322 100323 100324 100325 100326 100327
## [11311] 100328 100329 100330 100331 100332 100333 100334 100335 100336 100337
## [11321] 100338 100339 100340 100341 100342 100343 100344 100345 100346 100347
## [11331] 100348 100349 100350 100351 100352 100353 100354 100355 100356 100357
## [11341] 100358 100359 100360 100361 100362 100363 100364 100365 100366 100367
## [11351] 100368 100369 100370 100371 100372 100373 100374 100375 100376 100377
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## [11381] 100398 100399 100400 100401 100402 100403 100404 100405 100406 100407
## [11391] 100408 100409 100410 100411 100412 100413 100414 100415 100422 100423
## [11401] 100424 100425 100426 100427 100428 100429 100430 100431 100432 100433
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## [11471] 100494 100495 100496 100497 100498 100499 100500 100501 100502 100503
## [11481] 100504 100505 100506 100507 100508 100509 100510 100511 100512 100513
## [11491] 100514 100515 100516 100517 100518 100522 100523 100524 100525 100526
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## [11521] 100547 100548 100549 100550 100551 100552 100553 100554 100555 100556
## [11531] 100557 100558 100559 100560 100561 100562 100563 100564 100565 100566
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## [11551] 100579 100580 100581 100582 100583 100584 100585 100586 100587 100588
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## [11571] 100599 100600 100601 100602 100603 100604 100605 100606 100607 100612
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## [11641] 100673 100674 100675 100676 100677 100678 100679 100680 100681 100682
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## [11721] 100753 100754 100755 100756 100757 100758 100759 100760 100761 100762
## [11731] 100763 100764 100765 100766 100767 100768 100769 100770 100771 100772
## [11741] 100773 100774 100775 100776 100777 100778 100779 100780 100781 100782
## [11751] 100783 100784 100785 100786 100787 100788 100789 100790 100791 100792
## [11761] 100793 100794 100795 100796 100797 100798 100799 100800 100801 100802
## [11771] 100803 100804 100805 100806 100807 100808 100809 100810 100811 100812
## [11781] 100813 100814 100815 100816 100817 100818 100819 100820 100821 100822
## [11791] 100823 100824 100825 100826 100827 100828 100829 100830 100831 100832
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## [11841] 100873 100874 100875 100876 100877 100878 100879 100880 100881 100882
## [11851] 100883 100884 100885 100886 100887 100888 100889 100890 100891 100892
## [11861] 100895 100896 100897 100898 100899 100900 100901 100902 100903 100904
## [11871] 100905 100906 100907 100908 100909 100910 100911 100912 100913 100914
## [11881] 100915 100916 100917 100918 100919 100920 100921 100922 100923 100924
## [11891] 100925 100926 100927 100928 100929 100930 100931 100932 100933 100934
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## [11911] 100945 100946 100947 100948 100949 100950 100951 100952 100953 100954
## [11921] 100955 100956 100957 100958 100959 100960 100961 100962 100963 100964
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## [11941] 100975 100976 100977 100979 100980 100981 100982 100983 100984 100985
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## [12751] 101794 101795 101796 101797 101798 101799 101800 101801 101802 101803
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## [12771] 101814 101815 101816 101817 101818 101819 101820 101821 101822 101823
## [12781] 101824 101825 101826 101827 101828 101829 101830 101831 101832 101833
## [12791] 101834 101835 101836 101837 101843 101844 101845 101846 101847 101848
## [12801] 101849 101850 101851 101852 101853 101854 101855 101856 101857 101858
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## [12821] 101869 101870 101871 101872 101873 101874 101875 101876 101877 101878
## [12831] 101879 101880 101881 101882 101883 101884 101885 101886 101887 101888
## [12841] 101889 101890 101891 101892 101893 101894 101895 101896 101897 101898
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## [12871] 101920 101921 101922 101923 101924 101925 101926 101927 101928 101929
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## [13161] 102214 102215 102216 102217 102218 102219 102220 102221 102222 102223
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## [13231] 102703 102704 102713 102725 102729 102734 102735 102736 102737 102743
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## [13341] 103550 103565 103566 103592 103593 103594 103595 103609 103616 103641
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## [13491] 106553 106554 106580 106581 106587 106614 106616 106620 106621 106622
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## [14021] 114871 114872 114873 114874 114875 114876 114877 114901 114942 114956
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## [14111] 116075 116076 116094 116095 116106 116107 116115 116119 116121 116122
## [14121] 116129 116130 116134 116154 116160 116161 116162 116188 116189 116190
## [14131] 116202 116203 116204 116223 116225 116226 116229 116232 116241 116261
## [14141] 116266 116267 116268 116269 116278 116280 116283 116285 116286 116295
## [14151] 116296 116297 116307 116308 116309 116342 116363 116364 116365 116373
## [14161] 116382 116383 116388 116389 116390 116402 116404 116405 116406 116407
## [14171] 116408 116409 116411 116412 116413 116414 116415 116416 116424 116425
## [14181] 116465 116466 116467 116471 116486 116487 116488 116498 116499 116513
## [14191] 116514 116522 116553 116566 116567 116571 116572 116598 116599 116612
## [14201] 116613 116614 116615 116647 116671 116672 116673 116686 116687 116688
## [14211] 116689 116690 116691 116692 116704 116705 116709 116735 116743 116744
## [14221] 116745 116746 116747 116748 116749 116750 116751 116752 116753 116760
## [14231] 116761 116762 116763 116764 116765 116766 116767 116769 116770 116771
## [14241] 116772 116779 116780 116826 116827 116828 116853 116854 116858 116859
## [14251] 116860 116861 116862 116863 116864 116885 116900 116905 116913 116914
## [14261] 116915 116922 116923 116924 116933 117045 117067 117074 117075 117076
## [14271] 117077 117079 117109 117110 117111 117121 117122 117123 117124 117166
## [14281] 117167 117185 117197 117198 117219 117233 117234 117264 117275 117277
## [14291] 117278 117279 117280 117281 117282 117283 117284 117285 117286 117309
## [14301] 117310 117311 117328 117329 117330 117331 117343 117344 117345 117365
## [14311] 117374 117376 117377 117390 117392 117393 117433 117434 117449 117500
## [14321] 117516 117542 117543 117544 117545 117595 117607 117608 117609 117610
## [14331] 117611 117612 117613 117617 117625 117626 117627 117628 117629 117637
## [14341] 117643 117646 117760 117836 117837 117838 117843 118023 118024 118234
## [14351] 118236 118237 118238 118271 118311 118312 118413 118558 118559 118560
## [14361] 118561 118562 118563 118564 118623 118624 118625 118626 118627 118628
## [14371] 118629 118630 118676 118677 118678 118679 118680 118681 118682 118683
## [14381] 118684 118721 118722 118723 118724 118725 118726 118727 118728 118729
## [14391] 118730 118731 118732 118733 118734 118735 118737 118781 118851 118852
## [14401] 118853 118863 118864 118943 118944 118945 118946 118947 118949 118950
## [14411] 118951 118952 118953 118954 118955 118956 118957 119008 119142 119152
## [14421] 119153 119199 119200 119201 119202 119203 119285 119286 119387 119388
## [14431] 119572 119588 119589 119590 119609 119610 119611 119637 119673 119674
## [14441] 119743 119760 119761 119763 119764 119765 119766 119767 119781 119782
## [14451] 119783 119784 119785 119791 119796 119891 119892 119903 119964 119965
## [14461] 120117 120136 120238 120252 120253 120262 120263 120264 120265 120266
## [14471] 120267 120291 120292 120293 120329 120342 120431 120456 120457 120494
## [14481] 120495 120496 120544 120545 120546 120547 120548 120549 120550 120577
## [14491] 120581 120582 120583 120584 120585 120586 120587 120588 120601 120602
## [14501] 120603 120604 120758 120809 120832 120833 120834 120835 120836 120837
## [14511] 120838 120839 120840 120891 120953 120954 120955 120956 121001 121024
## [14521] 121025 121065 121081 121082 121186 121194 121203 121316 121317 121488
## [14531] 121520 121521 121523 121524 121525 121526 121527 121546 121566 121594
## [14541] 121634 121672 121680 121681 121689 121690 121694 121695 121696 121701
## [14551] 121710 121711 121712 121713 121714 121738 121739 121740 121789 121816
## [14561] 121833 121856 121857 121858 121861 121862 121863 121930 121931 121964
## [14571] 121965 121979 121980 121981 121982 121983 121984 121985 121986 122019
## [14581] 122046 122067 122077 122078 122079 122080 122081 122082 122083 122084
## [14591] 122152 122169 122170 122181 122182 122183 122219 122220 122258 122300
## [14601] 122301 122308 122312 122326 122327 122471 122481 122482 122483 122484
## [14611] 122485 122486 122487 122488 122530 122531 122532 122533 122541 122542
## [14621] 122596 122597 122598 122599 122600 122601 122602 122603 122604 122613
## [14631] 122614 122615 122640 122641 122667 122668 122677 122678 122709 122710
## [14641] 122711 122738 122761 122762 122763 122764 122765 122766 122767 122768
## [14651] 122769 122784 122785 122792 122820 122825 122826 122827 122854 122872
## [14661] 122873 122874 122879 122882 122883 122884 122885 122908 122909 122910
## [14671] 122911 122954 122994 123045 123046 123047 123048 123064 123065 123066
## [14681] 123067 123068 123069 123070 123071 123080 123092 123096 123097 123115
## [14691] 123132 123212 123213 123235 123236 123281 123282 123346 123347 123385
## [14701] 123386 123387 123388 123389 123390 123391 123417 123452 123453 123454
## [14711] 123455 123456 123575 123576 123577 123578 123682 123761 124011 124012
## [14721] 124013 124098 124099 124121 124150 124151 124667 124790 124791 124792
## [14731] 124793 124993 124994 124995 124996 124997 124998 124999 125000 125366
## [14741] 125367 125368 125369 125441 125493 125538 125539 125542 125543 125544
## [14751] 125545 125552 125553 125554 125690 125720 125764 125779 126079 126080
## [14761] 126088 126106 126107 126166 126211 126212 126318 126364 126392 126393
## [14771] 126394 126395 126396 126397 126398 126471 126472 126473 126495 126498
## [14781] 126499 126545 126596 126642 126740 126741 126742 126743 126811 126852
## [14791] 126915 126916 126917 126918 126919 126973 126990 127093 127270 127271
## [14801] 127272 127275 127307 127308 127310 127311 127312 127313 127314 127467
## [14811] 127468 127488 127852 127985 127986 127987 127988 127989 127990 128006
## [14821] 128039 128040 128041 128058 128113 128114 128203 128204 128205 128206
## [14831] 128207 128208 128209 128268 128269 128270 128271 128272 128273 128274
## [14841] 128275 128403 128404 128405 128406 128429 128594 128595 128596 128597
## [14851] 128598 128599 128600 128601 128602 128653 129032 129033 129135 129136
## [14861] 129137 129138 129139 129140 129141 129142 129143 129144 129145 129146
## [14871] 129169 129236 129237 129266 129267 129268 129269 129270 129282 129301
## [14881] 129306 129317 129318 129319 129320 129324 129335 129344 129348 129349
## [14891] 129362 129363 129364 129365 129380 129396 129397 129405 129406 129408
## [14901] 129409 129410 129411 129412 129414 129417 129422 129423 129425 129426
## [14911] 129427 129428 129429 129430 129439 129449 129494 129495 129496 129497
## [14921] 129505 129509 129510 129513 129514 129527 129528 129529 129532 129533
## [14931] 129536 129537 129538 129539 129540 129548 129549 129568 129569 129577
## [14941] 129578 129579 129582 129583 129584 129597 129598 129609 129610 129622
## [14951] 129630 129632 129633 129636 129643 129644 129645 129657 129663 129664
## [14961] 129665 129680 129681 129691 129692 129693 129695 129696 129697 129698
## [14971] 129699 129700 129701 129702 129711 129712 129713 129726 129732 129735
## [14981] 129739 129749 129762 129764 129771 129772 129781 129783 129786 129788
## [14991] 129789 129798 129799 129800 129810 129811 129812 129827 129840 129841
## [15001] 129842 129860 129863 129864 129868 129876 129885 129886 129891 129892
## [15011] 129893 129895 129905 129914 129915 129916 129917 129918 129919 129929
## [15021] 129930 129931 129935 129936 129937 129938 129950 129951 129952 129953
## [15031] 129954 129955 129956 129961 129974 129989 129990 130016 130017 130019
## [15041] 130020 130021 130025 130028 130040 130041 130042 130043 130071 130072
## [15051] 130074 130075 130098 130099 130101 130102 130104 130105 130108 130114
## [15061] 130115 130116 130117 130118 130130 130139 130140 130141 130168 130172
## [15071] 130173 130174 130175 130176 130188 130205 130206 130209 130212 130214
## [15081] 130222 130226 130227 130228 130229 130230 130231 130232 130233 130238
## [15091] 130246 130247 130248 130249 130263 130264 130265 130266 130267 130268
## [15101] 130269 130270 130284 130290 130295 130296 130297 130298 130299 130300
## [15111] 130301 130302 130303 130304 130305 130306 130307 130308 130309 130312
## [15121] 130313 130314 130315 130316 130317 130318 130319 130320 130336 130356
## [15131] 130357 130373 130374 130391 130392 130398 130399 130400 130403 130416
## [15141] 130424 130436 130454 130508 130517 130518 130519 130520 130521 130536
## [15151] 130548 130556 130557 130565 130566 130567 130570 130571 130572 130588
## [15161] 130589 130590 130591 130595 130612 130613 130614 130624 130625 130626
## [15171] 130627 130646 130659 130667 130682 130726 130727 130728 130767 130778
## [15181] 130780 130781 130782 130783 130784 130785 130786 130787 130796 130812
## [15191] 130813 130814 130826 130827 130831 130843 130844 130845 130846 130847
## [15201] 130848 130868 130871 130877 130893 130928 130929 130931 130932 130933
## [15211] 130936 130937 130938 130951 130952 130959 130960 130982 130983 130987
## [15221] 130990 130991 130997 130998 131003 131012 131013 131016 131017 131018
## [15231] 131033 131034 131035 131043 131044 131045 131046 131047 131048 131062
## [15241] 131063 131064 131065 131066 131067 131068 131069 131070 131071 131072
## [15251] 131073 131074 131075 131083 131084 131086 131087 131110 131111 131112
## [15261] 131128 131129 131130 131131 131132 131133 131146 131149 131168 131169
## [15271] 131170 131171 131172 131188 131195 131196 131197 131198 131199 131225
## [15281] 131239 131240 131246 131249 131253 131263 131273 131291 131292 131293
## [15291] 131294 131370 131398 131404 131425 131426 131437 131438 131439 131461
## [15301] 131478 131506 131507 131508 131547 131551 131586 131592 131593 131594
## [15311] 131610 131641 131642 131657 131658 131664 131684 131685 131686 131700
## [15321] 131701 131712 131715 131717 131718 131769 131770 131771 131797 131820
## [15331] 131821 131822 131837 131843 131844 131845 131846 131847 131848 131865
## [15341] 131897 131898 131899 131903 131945 131946 131959 131998 131999 132027
## [15351] 132028 132038 132044 132045 132046 132047 132059 132126 132127 132128
## [15361] 132129 132130 132131 132132 132133 132167 132179 132180 132181 132182
## [15371] 132183 132184 132185 132192 132193 132194 132195 132196 132197 132198
## [15381] 132199 132214 132215 132241 132242 132243 132244 132245 132246 132247
## [15391] 132248 132249 132267 132268 132285 132286 132290 132291 132292 132293
## [15401] 132294 132295 132296 132327 132328 132329 132345 132365 132383 132423
## [15411] 132424 132425 132426 132452 132453 132454 132455 132456 132457 132458
## [15421] 132459 132460 132465 132476 132477 132483 132499 132506 132507 132508
## [15431] 132509 132534 132575 132629 132630 132651 132665 132666 132709 132710
## [15441] 132711 132712 132713 132714 132715 132716 132743 132755 132756 132777
## [15451] 132797 132800 132802 132806 132817 132863 132881 132921 132932 132945
## [15461] 132962 133060 133061 133094 133095 133120 133140 133156 133159 133169
## [15471] 133176 133177 133178 133182 133202 133203 133220 133221 133222 133223
## [15481] 133224 133232 133249 133250 133251 133252 133254 133255 133258 133259
## [15491] 133260 133261 133266 133267 133268 133269 133270 133272 133284 133285
## [15501] 133286 133287 133288 133299 133311 133312 133313 133314 133327 133335
## [15511] 133363 133367 133368 133390 133407 133428 133429 133430 133431 133432
## [15521] 133433 133435 133436 133437 133454 133467 133468 133480 133509 133521
## [15531] 133522 133523 133538 133539 133563 133564 133565 133569 133584 133586
## [15541] 133587 133593 133620 133629 133630 133639 133641 133644 133646 133647
## [15551] 133651 133652 133653 133654 133655 133656 133657 133658 133671 133672
## [15561] 133673 133674 133675 133718 133726 133741 133751 133760 133765 133766
## [15571] 133767 133768 133769 133770 133793 133801 133807 133826 133827 133828
## [15581] 133847 133848 133850 133874 133875 133886 133900 133901 133908 133927
## [15591] 133928 133956 133957 134030 134031 134063 134064 134072 134121 134122
## [15601] 134123 134124 134125 134126 134127 134128 134153 134154 134155 134156
## [15611] 134157 134158 134159 134160 134161 134162 134163 134164 134165 134166
## [15621] 134167 134170 134171 134172 134173 134174 134175 134176 134177 134178
## [15631] 134187 134188 134189 134216 134231 134246 134256 134257 134258 134265
## [15641] 134274 134282 134295 134296 134312 134358 134359 134394 134399 134400
## [15651] 134401 134411 134412 134414 134428 134435 134436 134437 134438 134452
## [15661] 134466 134482 134483 134484 134485 134489 134490 134491 134504 134517
## [15671] 134527 134549 134550 134558 134559 134566 134567 134568 134584 134585
## [15681] 134649 134650 134672 134689 134694 134695 134706 134726 134729 134735
## [15691] 134739 134788 134789 134809 134810 134814 134815 134824 134830 134855
## [15701] 134856 134861 134862 134874 134920 134921 134941 134942 134950 134956
## [15711] 134966 135026 135027 135028 135029 135030 135088 135125 135292 135384
## [15721] 135385 135477 135513 135519 135568 135663 135918 136000 136013 136014
## [15731] 136015 136016 136017 136018 136019 136020 136082 136083 136084 136085
## [15741] 136086 136087 136088 136089 136090 136091 136092 136093 136094 136095
## [15751] 136096 136106 136118 136119 136120 136121 136122 136145 136175 136190
## [15761] 136281 136282 136283 136310 136311 136312 136313 136314 136315 136316
## [15771] 136317 136318 136364 136365 136366 136367 136369 136395 136433 136513
## [15781] 136514 136655 136693 136885 136927 137179 137653 137654 137785 137786
## [15791] 137942 137943 137944 137945 137946 137947 137948 137949 138011 138012
## [15801] 138013 138014 138015 138016 138017 138018 138019 138020 138021 138022
## [15811] 138023 138024 138025 138239 138240 138241 138242 138243 138244 138245
## [15821] 138246 138247 138385 138426 138442 138443 138477 138478 138479 138480
## [15831] 138489 138490 138491 138492 138493 138535 138536 138537 138538 138539
## [15841] 138540 138881 138882Remove individuals with >50% NAs
For our workflow, we’re going to want to find the NAs in each row of data, count them up, and if >50% of the SNPs are NA, then remove the entire row.
We could find the NAs in each row like this. First, find the NAs in row 1 and save it to a vector:
i_NAs01 <- find_NAs(bird_snps_num_t[1,])## Results: 10 NAs present
## .And figure how how many NAs there are with length()
length(i_NAs01)## [1] 10Then continue this many times:
i_NAs02 <- find_NAs(bird_snps_num_t[2,])## Results: 10 NAs present
## .i_NAs03 <- find_NAs(bird_snps_num_t[3,])## Results: 4 NAs present
## .i_NAs04 <- find_NAs(bird_snps_num_t[4,])## Results: 5 NAs present
## .by making a new vector for each row and updating the row number in the brackets. This would take a lot of time and be very prone to errors.
for() loops
This process of working on many rows is most easily done with a common programming approach called a for loop. The name at first doesn’t make sense; what it should be called is a “do something a bunch of times” loop.
It is called a “for” loop because you tell it something along the lines of: “FOR every row in this dataframe frame, do this …” In our case we’ll work on rows, but it can also work on columns, or anything else that can exist in R.
I’ll write a for() loop that will go through each row of
our SNP data and determine if >50% of the values are NA.
I’ll use our find_NA() function we just made.
To do this I’m going to want to have a few things:
N_rows: The total number of rows of data in our dataframeN_NA: A vector to hold how many NAs are in each rowN_SNPs: The total number of columns, so we can determine if >50% of the columns (SNPs) are NAs.
We can get the number of rows with nrow():
# call nrow() on bird_snps_num_t
N_rows <- nrow(bird_snps_num_t) # TODOWe can make a vector to store how many NAs are in each row like this,
where rep() repeats 0 for us as many times as we want.
N_NA <- rep(x = 0, times = N_rows)I can get the number of SNPs withncol()
# call ncol() on bird_snps_num_t
N_SNPs <- ncol(bird_snps_num_t) # TODOThe percentage of SNPs that are NA can be found as
length(i_NAs01)/N_SNPs*100## [1] 13.88889If we were doing this by hand we’d have to fill in the vector of the
number of NAs (N_NA) like this:
# Number of NAs in row 1
i_NAs01 <- find_NAs(bird_snps_num_t[1,])## Results: 10 NAs present
## .N_NA[1] <- length(i_NAs01)
# Number of NAs in row 2:
i_NAs02 <- find_NAs(bird_snps_num_t[2,])## Results: 10 NAs present
## .N_NA[2] <- length(i_NAs02)
# Number of NAs in row 3:.
# ... etcThat would not be fun. So we automate the process with a
for() loop. I won’t explain right now how whole thing work,
but take a look to get the general sense of what it is.
I’ll repeat the previous preparation code so its all in one place.
# N_rows
# number of rows (individuals)
N_rows <- nrow(bird_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(bird_snps_num_t)
# the for() loop
for(i in 1:N_rows){
# for each row, find the location of
## NAs with bird_snps_num_t()
i_NA <- find_NAs(bird_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: 10 NAs present
## .Results: 10 NAs present
## .Results: 4 NAs present
## .Results: 5 NAs present
## .Results: 5 NAs present
## .Results: 2 NAs present
## .Results: 2 NAs present
## .Results: 2 NAs present
## .Results: 5 NAs present
## .Results: 5 NAs present
## .Results: 7 NAs present
## .Results: 7 NAs present
## .Results: 7 NAs present
## .Results: 7 NAs present
## .Results: 5 NAs present
## .Results: 12 NAs present
## .Results: 3 NAs present
## .Results: 6 NAs present
## .Results: 12 NAs present
## .Results: 4 NAs present
## .Results: 4 NAs present
## .Results: 12 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 5 NAs present
## .Results: 2 NAs present
## .Results: 8 NAs present
## .Results: 7 NAs present
## .Results: 7 NAs present
## .Results: 7 NAs present
## .Results: 9 NAs present
## .Results: 9 NAs present
## .Results: 3 NAs present
## .Results: 5 NAs present
## .Results: 3 NAs present
## .Results: 12 NAs present
## .Results: 10 NAs present
## .Results: 4 NAs present
## .Results: 6 NAs present
## .Results: 4 NAs present
## .Results: 4 NAs present
## .Results: 4 NAs present
## .Results: 5 NAs present
## .Results: 6 NAs present
## .Results: 6 NAs present
## .Results: 4 NAs present
## .Results: 7 NAs present
## .Results: 6 NAs present
## .Results: 6 NAs present
## .Results: 16 NAs present
## .Results: 3 NAs present
## .Results: 11 NAs present
## .Results: 10 NAs present
## .Results: 4 NAs present
## .Results: 14 NAs present
## .Results: 3 NAs present
## .Results: 6 NAs present
## .Results: 2 NAs present
## .Results: 4 NAs present
## .Results: 10 NAs present
## .Results: 2 NAs present
## .Results: 9 NAs present
## .Results: 9 NAs present
## .Results: 14 NAs present
## .Results: 12 NAs present
## .Results: 6 NAs present
## .Results: 10 NAs present
## .Results: 7 NAs present
## .Results: 7 NAs present
## .Results: 7 NAs present
## .Results: 12 NAs present
## .Results: 17 NAs present
## .Results: 17 NAs present
## .Results: 15 NAs present
## .Results: 6 NAs present
## .Results: 4 NAs present
## .Results: 2 NAs present
## .Results: 17 NAs present
## .Results: 8 NAs present
## .Results: 5 NAs present
## .Results: 5 NAs present
## .Results: 3 NAs present
## .Results: 5 NAs present
## .Results: 5 NAs present
## .Results: 4 NAs present
## .Results: 4 NAs present
## .Results: 4 NAs present
## .Results: 14 NAs present
## .Results: 8 NAs present
## .Results: 4 NAs present
## .Results: 2 NAs present
## .Results: 3 NAs present
## .Results: 3 NAs present
## .Results: 3 NAs present
## .Results: 4 NAs present
## .Results: 2 NAs present
## .Results: 2 NAs present
## .Results: 10 NAs present
## .Results: 8 NAs present
## .Results: 3 NAs present
## .Results: 8 NAs present
## .Results: 9 NAs present
## .Results: 9 NAs present
## .Results: 13 NAs present
## .Results: 10 NAs present
## .Results: 9 NAs present
## .Results: 9 NAs present
## .Results: 9 NAs present
## .Results: 9 NAs present
## .Results: 9 NAs present
## .Results: 5 NAs present
## .Results: 5 NAs present
## .Results: 5 NAs present
## .Results: 5 NAs present
## .Results: 5 NAs present
## .Results: 19 NAs present
## .Results: 19 NAs present
## .Results: 19 NAs present
## .Results: 19 NAs present
## .Results: 13 NAs present
## .Results: 10 NAs present
## .Results: 4 NAs present
## .Results: 4 NAs present
## .Results: 4 NAs present
## .Results: 4 NAs present
## .Results: 4 NAs present
## .Results: 8 NAs present
## .Results: 8 NAs present
## .Results: 12 NAs present
## .Results: 2 NAs present
## .Results: 2 NAs present
## .Results: 2 NAs present
## .Results: 8 NAs present
## .Results: 10 NAs present
## .Results: 9 NAs present
## .Results: 2 NAs present
## .Results: 2 NAs present
## .Results: 5 NAs present
## .Results: 4 NAs present
## .Results: 9 NAs present
## .Results: 2 NAs present
## .Results: 13 NAs present
## .Results: 4 NAs present
## .Results: 3 NAs present
## .Results: 3 NAs present
## .Results: 3 NAs present
## .Results: 3 NAs present
## .Results: 3 NAs present
## .Results: 8 NAs present
## .Results: 13 NAs present
## .Results: 13 NAs present
## .Results: 4 NAs present
## .Results: 4 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 4 NAs present
## .Results: 17 NAs present
## .Results: 17 NAs present
## .Results: 4 NAs present
## .Results: 15 NAs present
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## .Results: 3 NAs present
## .Results: 3 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 5 NAs present
## .Results: 2 NAs present
## .Results: 2 NAs present
## .Results: 2 NAs present
## .Results: 3 NAs present
## .Results: 4 NAs present
## .Results: 4 NAs present
## .Results: 4 NAs present
## .Results: 5 NAs present
## .Results: 5 NAs present
## .Results: 5 NAs present
## .Results: 6 NAs present
## .Results: 6 NAs present
## .Results: 15 NAs present
## .Results: 15 NAs present
## .Results: 16 NAs present
## .Results: 16 NAs present
## .Results: 16 NAs present
## .Results: 16 NAs present
## .Results: 16 NAs present
## .Results: 16 NAs present
## .Results: 16 NAs present
## .Results: 16 NAs present
## .Results: 16 NAs present
## .Results: 16 NAs present
## .Results: 16 NAs present
## .Results: 17 NAs present
## .Results: 5 NAs present
## .Results: 4 NAs present
## .Results: 3 NAs present
## .Results: 3 NAs present
## .Results: 3 NAs present
## .Results: 2 NAs present
## .Results: 2 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 6 NAs present
## .Results: 6 NAs present
## .Results: 3 NAs present
## .Results: 3 NAs present
## .Results: 3 NAs present
## .Results: 2 NAs present
## .Results: 6 NAs present
## .Results: 6 NAs present
## .Results: 8 NAs present
## .Results: 10 NAs present
## .Results: 2 NAs present
## .Results: 4 NAs present
## .Results: 15 NAs present
## .Results: 5 NAs present
## .Results: 5 NAs present
## .Results: 13 NAs present
## .Results: 13 NAs present
## .Results: 13 NAs present
## .Results: 13 NAs present
## .Results: 13 NAs present
## .Results: 13 NAs present
## .Results: 13 NAs present
## .Results: 13 NAs present
## .Results: 4 NAs present
## .Results: 6 NAs present
## .Results: 5 NAs present
## .Results: 5 NAs present
## .Results: 9 NAs present
## .Results: 9 NAs present
## .Results: 9 NAs present
## .Results: 10 NAs present
## .Results: 9 NAs present
## .Results: 9 NAs present
## .Results: 2 NAs present
## .Results: 9 NAs present
## .Results: 2 NAs present
## .Results: 10 NAs present
## .Results: 6 NAs present
## .Results: 6 NAs present
## .Results: 2 NAs present
## .Results: 2 NAs present
## .Results: 13 NAs present
## .Results: 9 NAs present
## .Results: 9 NAs present
## .Results: 9 NAs present
## .Results: 15 NAs present
## .Results: 15 NAs present
## .Results: 15 NAs present
## .Results: 8 NAs present
## .Results: 6 NAs present
## .Results: 6 NAs present
## .Results: 6 NAs present
## .Results: 6 NAs present
## .Results: 6 NAs present
## .Results: 12 NAs present
## .Results: 5 NAs present
## .Results: 4 NAs present
## .Results: 4 NAs present
## .Results: 16 NAs present
## .Results: 16 NAs present
## .Results: 9 NAs present
## .Results: 3 NAs present
## .Results: 6 NAs present
## .Results: 15 NAs present
## .Results: 7 NAs present
## .Results: 11 NAs present
## .Results: 21 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 16 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 11 NAs present
## .Results: 27 NAs present
## .Results: 28 NAs present
## .Results: 18 NAs present
## .Results: 29 NAs present
## .Results: 29 NAs present
## .Results: 29 NAs present
## .Results: 29 NAs present
## .Results: 29 NAs present
## .My vector N_SNPs now how the number of NAs in each row
of the dataframe.
head(N_NA)## [1] 10 10 4 5 5 2We can get a sense of the how many NAs there are in the rows of the dataset by making a histogram. Most rows have very few, and a few have a lot:
# Call hist() on N_NA
hist(N_NA) # TODO
The authors of the bird speciation paper decided to remove any row that was >50% NAs. There are 1929 SNPs, so 50% is about 964 SNPs.
# total number of columns
N_SNPs## [1] 72# 50% of N_SNPs
cutoff50 <- N_SNPs*0.5I can add a line for the cutoff to the plot with
abline()
# Call hist() on N_NA
## add a vertical line at the cutoff value
## using abline()
hist(N_NA) # TODO
abline(v = cutoff50,
col = 2,
lwd = 2,
lty = 2)
After figuring out how many NAs there in each row, I can convert this to a percent.
percent_NA <- N_NA/N_SNPs*100I can plot these percentages and set the cutoff at 50 for 50%
# Call hist() on N_NA
## add a vertical line at 50%
## using abline()
hist(percent_NA) # TODO
abline(v = cutoff50 , # TODO
col = 2,
lwd = 2,
lty = 2)
I can determine the index value of each row with >50% NAs using
which()
# Call which() on percent_NA
i_NA_50percent <- which(percent_NA > 50) # TODOI use length() to see how many there are
# call length() on i_NA_50percent
length(i_NA_50percent) # TODO## [1] 0The index values happen to be:
i_NA_50percent## integer(0)There are 4 rows where 50% or more of the columns contain an NA
In the paper they say they removed 6, and I’m not sure where the discrepancy comes from. In order get up to 6 birds, I need to decrease the threshold to 38% missing.
which(percent_NA > 38)## [1] 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066
## [16] 1537 1538 1539 1540 1541 1542 1543 1544 1923 1925 1926 1927 1928 1929length(which(percent_NA > 38))## [1] 29Remove rows with >50% missing
I can remove the rows of data with >50% missing using negative indexing.
bird_snps_num_t02 <- bird_snps_num_t[-i_NA_50percent, ]I always need to check to make sure the previous and current data make sense.
dim(bird_snps_num_t)## [1] 1929 72dim(bird_snps_num_t02)## [1] 0 72Determine sampling locations
In our workflow information about the samples like their population of origin is getting embedded in the row names of the dataframe. (In contrast to this, VCF files from the 1000 Genomes Project have a separate file with all the information).
Its going to become necessary in subsequent assignments to access this information, for example to color-code plots. It takes a little bit of code to get the information from these row names, so I’m not going to dig into it here except to say I’m using functions known as regular expressions to be able to edit the text in the row names.
First, let’s look at the row names.
# call row.names() on bird_snps_num_t
row_names <- row.names(bird_snps_num_t) # TODO
# call head() on row_names
head(row_names) # TODO## NULLThe individual samples are called things like “Nel3” and “Cau10”. The numbers are ID numbers of individuals birds that DNA was collected from, and the letters are the populations.
I can use regular expressions (in this case a function called
gsub()) to remove the stuff like “sample_ACAAA_” before the
things I want. First I’ll remove the “sample_” (don’t worry about the
exact details of how the function works).
# add gsub() to before ("sample_","",row_names)
row_names02 <- gsub("sample_","",row_names)
# look at the output using head()
head(row_names02)## character(0)Now I’ll get rid of the As, Cs, Ts and Gs (not yet sure what those
are actually…). This gives me a unique combination of a population code
and number for each sample. (Again, we won’t worry about the code
withing gsub()).
# clean up the character data
sample_id <- gsub("^([ATCG]*)(_)(.*)",
"\\3",
row_names02)
# look at thee output
head(sample_id)## character(0)Now I want a vector just with the population code, so I’ll use
gsub() to get rid of the numbers. (Again, don’t worry about
the details of what’s in gsub().)
# add gsub() before the stuff in the parentheses
pop_id <- gsub("[01-9]*", # TODO
"",
sample_id)The function table() summarizes the output for me
# call table() on pop_id
table(pop_id) # TODO## < table of extent 0 >Back to the issue of the number of rows with >50% NAs
As noted above, the authors say they removed 6 rows because of NAs, but I only got 4. Its actually pretty common for things reported in a paper to diverge from what you’re able to replicate from the data - somewhere, something minor got misreported or left off of a file. But I do always like to try to figure out what’s going on.
The author’s state:
“We obtained blood samples from 75 Ammodramus sparrows … 15 from each of five putative subspecies. … Due to missing data, we removed six individuals (four of which were from [the subspecies] subvirgatus ), resulting in the analysis of 69 individuals (11–15 individuals per population).
Now that I’ve extracted the information on the samples I can see what samples they provided in their data.
Again, I can summarize the vector of population names with
table().
length(pop_id)## [1] 0table(pop_id)## < table of extent 0 >Right away I can see I have only 72 samples versus their 75, so 3 are missing. There’s also only 13 in the “Cau” category and 1 in “Sub”. So the .vcf file they provided is either missing a few birds, or something is happening when vcfR loads to kick out some rows, perhaps due to data quality. I could open up the vcfR file in a text editor to check this out if I wanted.
When locating rows with NAs I created a vector where there were >50% NAs:
i_NA_50percent## integer(0)I can compare this to my vector of population IDs using brackets:
sample_id[i_NA_50percent]## character(0)In the paper they say of the six samples they removed, “four of which were from [the subspecies] subvirgatus”. I have 3 samples called “Sub”, which are probably 3 of those 4 samples, and one “Cau.”
In total, I’m missing 1 Sub with >50% missing data, 1 Cau with >50% missing data, and 1 Cau with <50% missing data. I’m not sure what’s going on, but I doubt this will impact the analysis.