Exam
Aleksandra Atanasova
2025-02-13
Evolutionary Genetics
1)
Construct a phylogenetic tree using Bayesian inference and explain your results (relations between observed taxa). How does the method you used differ from the Maximum likelihood method?
The Bayesian phylogenetic tree shows the evolutionary relationships between different lizards that from two major families, Gymnophthalmidae and Alopoglossidae.
At the base of the tree, there’s a split between two main lineages: 1. Alopoglossus species, A. atriventris and A. carninicaudatus 2. Another leading to all other taxa shown
Alopoglossus species A.atriventris and A.carinicaudatus, form a well-supported monophyletic clade which means they share a recent common ancestor.
Arthrosaura reticulata and related species, Anotosaura sp., A.vanzolinia, Leposoma percarinatum and Ecpleopus gaudichausii also form a distinct cluster, and have close evolutionary relationship.
Colobosaurinae taxa, including Colobosaurus mentalis, Nothobachia ablephara, Calyptommatus and Micrablepharus, form another well-supported clade.
The most late derived groups include Prionodactylus oshaughnessyi, Prionodactylus argulus, Pantodactylus schreibersii schreibersii.
The genus Prionodactylus, including P.oshaughnessyi and P.argulus is well-separated but still related to Bachia dorbignyi, showing deeper evolutionary divergence.
The tree topology supports the relationships among these taxa, but some branches have lower support values like 0.5228, 0.3992, 0.4944.
Bayesian inference trees incorporate prior beliefs and assumptions about the evolutionary model, using the Bayes‘ theorem. The resulting initial probabilities are based on previously observed data and the constructed tree topology stems from prior assumptions (known as posterior distribution). It functions in three steps: 1. All initially constructed trees are equally probable 2. Prior information and observarions are considered, some are more probable than others 3. A posterior probability is calculated (using Bayes‘ theorem), combining the probability of prior observations and the probability of their trees
ML depends on a stohastic (random) evolutionary model for nucleotide and amino acid substitution. The ML approach estimates its own paramaters by searching for what values seem most probable and contain the fewest mutations/changes; it first draws out a tree, randomly redistributes its branches and compares the two versions, then keeps the more likely one.
BI is slower, more complex and computationally demanding, assuming BI‘s prior data is reliable and not flawed.It is preferred when dealing with small datasets, complex models, and cases where prior information is available.
ML does not incorporate prior data and is usually faster and less resource intensive, however, because of that, it‘s also more prone to biases.It is useful when computational efficiency is a concern.
2)
While working in the field you found an unknown eDNA sample. After a thorough genetic analysis, you’ve discovered the following sequence. Which species does the sample belong to?
1 aatattatac tttatttttg ctatatgatc aggaataatt ggttcatcta taagattatt
61 aattcgaata gaattaagac atccaggtat atgaattaat aatgatcaaa tttataattc
121 tttagtaaca agacatgcat ttttaataat tttttttata gttatacctt ttataattgg
181 tggatttgga aattatctaa ttccattaat attaggatcc ccagatatag cttttcctcg
241 aataaataat attagatttt gacttctacc tccatcatta ttcatattat tattaagaaa
301 tatatttaca cctaatgtag gtacaggatg aactgtatat cctcctttat cttcttattt
361 atttcattca tcaccttcaa ttgatattgc aattttttct ttacatatat caggaatctc
421 ttcaattatt ggatcattaa attttatcgt tactatttta ttaataaaaa atttttcatt
481 aaattatgat caaattaatt tattttcatg atcagtatgt attacagtaa ttttattaat
541 tctatcttta ccagtattag ccggtgcaat tactatatta ttatttgatc gaaattttaa
601 tacttcattt tttgacccaa taggaggagg agacccaatc ctttatcaac atttatttDoing Blast Nucleotide I got the organism Bombus terrestris.
Does it have a reference genome published?
We can see that in the entries we got, we have accession numbers that have prefix NC, which stands for RefSeq (Reference Sequence) entries and they are reference genomes or at least very reliable and complete genomes. In GenBank, we can check in description: Bombus terrestris lusitanicus mitochondrion, complete genome.
Is the species endangered?
The species is not currently at risk of extinction.
What is its whole taxonomic classification?
We can check on NCBI taxonomy.
Eukaryota – Superkingdom Opisthokonta – Clade Metazoa - Kingdom
Eumetazoa, Bilateria, Protostomia, Ecdysozoa, Panarthropoda – Clades
Arthropoda – Phylum Mandibulata, Pancrustacea – Clades Hexapoda –
Subphylum Insecta – Class Dicondylia – Clade Pterygota – Subclass
Neoptera – Infraclass Endopterygota – Cohort Hymenoptera - Order
Apocrita – Suborder Aculeata – Infraorder Apoidea – Superfamily
Anthophila – Clade Apidae – Family Apinae – Subfamily Bombini – Tribe
Bombus – Genus Bombus - Subgenus
3)
Take a look at the provided haplotype network. What conclusions can you draw about the observed species based on the information provided by the network?
There are three major groups. Each group has a larger haplotype. These haplotypes are most common and ancestral in the regions they are from.
Moroccan haplotypes and haplotypes from La Palma and Iberia are separated by 14 substitutions, indicating genetic distance from the other groups.
La Palma shows a high level of genetic variation with multiple haplotypes, including H1, H37, H38, and others. Some haplotypes like H1, H15 are shared with Iberia which represents common ancestry.
Iberia shows a central haplotype H2 with a lot of closely related haplotypes in a star-like pattern with few mutations. This is probably caused by founder effect, followed by expansion.
Morocco also forms a distinct genetic cluster, with H47 as a central haplotype and multiple smaller ones. It is an isolated genetic lineage indicated by the large genetic distance from the other groups which is probably due to long period of isolation because of geographical barriers, like the Gibraltar which limits gene flow between Iberian and Morrocan populations.
Probably the ancestors are from Morroco, and some individuals passed the Gibraltar and arrived in Iberia which caused founder effect.The surviving individuals formed the central haplotype H2. Different individuals aquired new mutations, forming closely related, newly derived haplotypes, hence the star-shaped pattern.
4)
How would you define the phylogenetic relationships on the tree? How reliable are your results, and what threshold would you set for reliable support in your analysis? What could you do to improve the results – would you exclude any taxa/species/samples or add new data from genetic databases?
The ESS values are acceptable in Tracer. Some nodes have weakly supported clades, which indicate phylogenetic uncertainty. The confidence value threshold is 0.95, and is tolerable till 0.7 or 0.6. Any node below the threshold is not reliable.
We can improve the results with adding more genetic data to increase resolution, like closely related species or we can also remove some species to test robustness. We also can exclude taxa with poor sequencing data.
5)
Your dataset is defined by a single locus or molecular marker. Which molecular markers would you use if you wanted to examine closer or more distant phylogenetic relationships within a species or genus? Would you change the model in this case, and do you think it is possible to use multiple markers? If so, which markers are available and would be useful for this purpose?
For closer phylogenetic relationships within a species or genus we can use: microsatellites, SNPs. For distant phylogenetic relationships within a species or genus we can use rRNAs: 18S rRNA.
It is possible to use more markers and we would need to change the model.
6)
How many S (singleton), C (conserved), V (variable) and Pi (Parsimony – informative) sites did your alignment have? What do these values tell us? For the purpose of our analyses, are singleton or parsimony-informative sites more informative? Why?
S (Singleton): 42/629 C (Conserved): 280/629 V (Variable): 341/629 Pi (Parsimony informative): 299/629
S are sites where only one sequence in the dataset has a unique mutation, they occur only once in the alignment and are not useful for our analysis because they do not provide shared variation between the taxa.
C are sites that remain unchanged across all sequences. They are not informative for phylogeny, but useful for identifying highly conserved regions.
V are positions where at least two different nucleotides appear in the alignment, but not all variable sites are phylogenetically informative.
Pi are sites where at least two different nucleotides appear in at least two different sequences. These are most useful for phylogeny because they help define evolutionary relationships.
High number of Pi sites shows that the dataset contains enough information to construct a reliable tree. Low number of singletons indicates that sequencing errors or unique mutations will not be present in the dataset. The relatively high number of conserved sites (280/629) shows that some regions of the sequence are functionally fixed and not evolving rapidly.
Pi sites are more informative than singleton sites because they provide shared variation, which means they occur in multiple taxa and help build evolutionary relationships, allowing the model to detect patterns of common ancestry. Singletons do not contribute to tree structure, since they appear only in one sequence.
7)
Which is the optimal model for the construction of your phylogenetic tree according to the BIC criterium? Do the BIC and AIC criteria result in identical trees?
Population genetics
library(dartR)
# library(adegenet)
library(SNPRelate)
library(HardyWeinberg)
library(ggtern)
library(dartRverse)
library(reshape2)
library(seqinr)
library(MultiPhen)
library(tidyverse)
library(pegas)
library(hierfstat)1.
After sequencing and bioinformatics analysis, you have a set of SNPs that you want to filter for further analysis. The species you are studying has 26 chromosome pairs. You want to exclude all loci that have more than 2% missing data and all individuals that have more than 4% missing genotype. You also want to exclude all loci that have a minor allele frequency below 2%. Construct a PLINK command that will filter your hypothetical binary file “data_SNP_4.bed” by the desired parameters.
Since this is a hypothetical file, I did the analysis on actual files we have from exercises. I include also screenshots to prove the command is working.
This is the command I used with my files.
system("plink2 --bfile bed_TEST_EXAM --geno 0.02 --mind 0.04 --maf 0.02 --make-bed --out bed_filtered_EXAM")## [1] 3
This is the hypothetical command with the hypothetical file.
system("plink2 --bfile data_SNP_4 --geno 0.02 --mind 0.04 --maf 0.02 --make-bed --out data_SNP_4_filtered")2.
How many individuals, populations, loci do you have in your dataset? Which populations do you have, please give the names. Which command did you use to do this? Before proceeding you need to run another command to check the validity of the data. What is this command?
We will first import all the files we have, so we have all the data prepared at start.
# Load the raw data
raw_data <- read.table("D.raw", header=TRUE, stringsAsFactors=FALSE)
head(raw_data)## FID IID PAT MAT SEX PHENOTYPE AX.93233744_C_0 AX.93233744_C_HET
## 1 Mel 1_3 0 0 0 -9 0 0
## 2 Mel 2_3 0 0 0 -9 0 0
## 3 Mel 3_2 0 0 0 -9 0 0
## 4 Mel 5_1 0 0 0 -9 0 0
## 5 Mel 8_1 0 0 0 -9 0 0
## 6 Mel 9_1 0 0 0 -9 0 0
## AX.93233745_T_C AX.93233745_T_HET AX.93233746_A_C AX.93233746_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93233747_C_C AX.93233747_C_HET AX.93233749_G_C AX.93233749_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93233752_G_C AX.93233752_G_HET AX.93233753_T_C AX.93233753_T_HET
## 1 0 0 0 0
## 2 1 1 2 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 2 0
## 6 0 0 0 0
## AX.93233757_C_C AX.93233757_C_HET AX.93233758_A_C AX.93233758_A_HET
## 1 0 0 2 0
## 2 0 0 0 0
## 3 0 0 2 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93233759_T_C AX.93233759_T_HET AX.93233760_G_C AX.93233760_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 1 1 1 1
## AX.93233761_C_C AX.93233761_C_HET AX.93233762_A_C AX.93233762_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 1 1 1 1
## AX.93233766_C_C AX.93233766_C_HET AX.93233767_A_C AX.93233767_A_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 0 0 0 0
## 4 1 1 1 1
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93233769_G_C AX.93233769_G_HET AX.93233773_C_C AX.93233773_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 1 1
## 5 1 1 0 0
## 6 1 1 1 1
## AX.93233776_A_C AX.93233776_A_HET AX.93218145_C_C AX.93218145_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93218143_A_C AX.93218143_A_HET AX.93218141_G_C AX.93218141_G_HET
## 1 0 0 2 0
## 2 0 0 1 1
## 3 0 0 2 0
## 4 1 1 2 0
## 5 0 0 1 1
## 6 1 1 1 1
## AX.93218140_A_C AX.93218140_A_HET AX.93218138_G_C AX.93218138_G_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 2 0 0 0
## AX.93218136_T_C AX.93218136_T_HET AX.93218134_T_C AX.93218134_T_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 2 0 0 0
## 5 0 0 NA NA
## 6 2 0 0 0
## AX.93218132_T_C AX.93218132_T_HET AX.93218131_T_C AX.93218131_T_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93218130_C_C AX.93218130_C_HET AX.93218128_A_C AX.93218128_A_HET
## 1 2 0 0 0
## 2 0 0 0 0
## 3 2 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93218124_C_C AX.93218124_C_HET AX.93218123_C_C AX.93218123_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93218122_T_0 AX.93218122_T_HET AX.93218120_T_C AX.93218120_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93218119_G_C AX.93218119_G_HET AX.93218117_A_C AX.93218117_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93218114_T_C AX.93218114_T_HET AX.93218113_A_C AX.93218113_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93218112_C_C AX.93218112_C_HET AX.93218108_C_C AX.93218108_C_HET
## 1 1 1 0 0
## 2 2 0 1 1
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93218104_A_C AX.93218104_A_HET AX.93218102_T_C AX.93218102_T_HET
## 1 1 1 0 0
## 2 2 0 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 1 1
## 6 1 1 0 0
## AX.93218101_T_C AX.93218101_T_HET AX.93218099_A_C AX.93218099_A_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 0 0 1 1
## 5 2 0 0 0
## 6 0 0 0 0
## AX.93218096_T_C AX.93218096_T_HET AX.93218094_T_C AX.93218094_T_HET
## 1 1 1 1 1
## 2 0 0 0 0
## 3 1 1 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93218093_A_C AX.93218093_A_HET AX.93218090_A_C AX.93218090_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 2 0
## 6 0 0 0 0
## AX.93218088_C_C AX.93218088_C_HET AX.93218085_C_C AX.93218085_C_HET
## 1 0 0 1 1
## 2 1 1 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 1 1 0 0
## AX.93218083_T_C AX.93218083_T_HET AX.93218078_G_C AX.93218078_G_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 0 0 0 0
## 4 1 1 1 1
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93218077_A_C AX.93218077_A_HET AX.93218076_T_C AX.93218076_T_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 2 0
## AX.93218075_T_C AX.93218075_T_HET AX.93218074_C_C AX.93218074_C_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 1 1 1 1
## 5 1 1 0 0
## 6 2 0 0 0
## AX.93218069_T_C AX.93218069_T_HET AX.93236500_A_C AX.93236500_A_HET
## 1 0 0 2 0
## 2 0 0 0 0
## 3 0 0 2 0
## 4 2 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93236494_C_C AX.93236494_C_HET AX.93236486_C_C AX.93236486_C_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93236480_G_C AX.93236480_G_HET AX.93254647_T_C AX.93254647_T_HET
## 1 1 1 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 1 1
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93254648_T_C AX.93254648_T_HET AX.93254654_A_C AX.93254654_A_HET
## 1 1 1 0 0
## 2 1 1 1 1
## 3 1 1 0 0
## 4 0 0 1 1
## 5 2 0 0 0
## 6 2 0 0 0
## AX.93254655_T_C AX.93254655_T_HET AX.93254656_G_C AX.93254656_G_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 1 1 0 0
## 5 0 0 2 0
## 6 0 0 2 0
## AX.93254657_C_C AX.93254657_C_HET AX.93254662_C_C AX.93254662_C_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93254663_A_C AX.93254663_A_HET AX.93254666_C_C AX.93254666_C_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93254667_T_C AX.93254667_T_HET AX.93238155_G_C AX.93238155_G_HET
## 1 0 0 2 0
## 2 0 0 1 1
## 3 0 0 2 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93238156_G_C AX.93238156_G_HET AX.93238157_A_C AX.93238157_A_HET
## 1 1 1 0 0
## 2 0 0 2 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 2 0 0 0
## 6 2 0 0 0
## AX.93238159_A_C AX.93238159_A_HET AX.93238163_G_C AX.93238163_G_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 1 1 2 0
## 5 0 0 0 0
## 6 1 1 2 0
## AX.93238165_G_C AX.93238165_G_HET AX.93238168_C_C AX.93238168_C_HET
## 1 0 0 0 0
## 2 0 0 2 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93238172_A_C AX.93238172_A_HET AX.93218021_G_C AX.93218021_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93238178_T_C AX.93238178_T_HET AX.93238179_G_C AX.93238179_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93238180_A_C AX.93238180_A_HET AX.93238183_C_A AX.93238183_C_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 1 1
## 6 0 0 2 0
## AX.93238186_T_C AX.93238186_T_HET AX.93238187_T_C AX.93238187_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93238188_A_0 AX.93238188_A_HET AX.93238191_G_0 AX.93238191_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93238192_C_C AX.93238192_C_HET AX.93238193_C_C AX.93238193_C_HET
## 1 0 0 0 0
## 2 NA NA 1 1
## 3 0 0 0 0
## 4 1 1 1 1
## 5 1 1 1 1
## 6 2 0 2 0
## AX.93238194_C_C AX.93238194_C_HET AX.93238197_A_C AX.93238197_A_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 0 0
## 6 2 0 0 0
## AX.93238199_G_C AX.93238199_G_HET AX.93243228_C_C AX.93243228_C_HET
## 1 1 1 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 NA NA 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93243229_A_C AX.93243229_A_HET AX.93243232_G_C AX.93243232_G_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 2 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93243238_G_C AX.93243238_G_HET AX.93243240_T_C AX.93243240_T_HET
## 1 0 0 1 1
## 2 1 1 2 0
## 3 0 0 1 1
## 4 2 0 0 0
## 5 1 1 1 1
## 6 1 1 1 1
## AX.93243241_T_C AX.93243241_T_HET AX.93243242_G_C AX.93243242_G_HET
## 1 1 1 1 1
## 2 1 1 0 0
## 3 1 1 1 1
## 4 0 0 0 0
## 5 1 1 1 1
## 6 1 1 0 0
## AX.93243244_A_C AX.93243244_A_HET AX.93243248_A_C AX.93243248_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93243252_A_C AX.93243252_A_HET AX.93243255_T_C AX.93243255_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 2 0
## AX.93243260_A_C AX.93243260_A_HET AX.93243262_A_C AX.93243262_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93243263_C_C AX.93243263_C_HET AX.93243266_G_C AX.93243266_G_HET
## 1 1 1 0 0
## 2 2 0 0 0
## 3 1 1 0 0
## 4 2 0 0 0
## 5 1 1 1 1
## 6 0 0 0 0
## AX.93255363_A_C AX.93255363_A_HET AX.93255362_C_C AX.93255362_C_HET
## 1 0 0 1 1
## 2 1 1 1 1
## 3 0 0 1 1
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93255361_A_C AX.93255361_A_HET AX.93255360_T_C AX.93255360_T_HET
## 1 2 0 1 1
## 2 1 1 2 0
## 3 2 0 1 1
## 4 0 0 2 0
## 5 0 0 1 1
## 6 1 1 0 0
## AX.93247298_A_C AX.93247298_A_HET AX.93247299_C_C AX.93247299_C_HET
## 1 0 0 1 1
## 2 2 0 0 0
## 3 0 0 1 1
## 4 0 0 2 0
## 5 NA NA 0 0
## 6 0 0 0 0
## AX.93247301_C_C AX.93247301_C_HET AX.93247304_A_C AX.93247304_A_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93247306_G_C AX.93247306_G_HET AX.93247307_G_C AX.93247307_G_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93247310_A_C AX.93247310_A_HET AX.93247311_T_C AX.93247311_T_HET
## 1 0 0 1 1
## 2 1 1 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 1 1 0 0
## AX.93247313_A_C AX.93247313_A_HET AX.93247319_C_C AX.93247319_C_HET
## 1 1 1 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 2 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93247323_T_C AX.93247323_T_HET AX.93247324_T_C AX.93247324_T_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 1 1
## AX.93247326_T_C AX.93247326_T_HET AX.93247327_G_C AX.93247327_G_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93247328_G_C AX.93247328_G_HET AX.93242996_G_C AX.93242996_G_HET
## 1 0 0 2 0
## 2 0 0 1 1
## 3 0 0 2 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 1 1 1 1
## AX.93243002_G_C AX.93243002_G_HET AX.93243004_G_C AX.93243004_G_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 1 1 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93243007_C_C AX.93243007_C_HET AX.93243008_T_C AX.93243008_T_HET
## 1 0 0 0 0
## 2 1 1 2 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93243009_G_C AX.93243009_G_HET AX.93243010_A_C AX.93243010_A_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93243012_T_C AX.93243012_T_HET AX.93243014_A_C AX.93243014_A_HET
## 1 0 0 1 1
## 2 0 0 2 0
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93243017_G_C AX.93243017_G_HET AX.93243021_A_C AX.93243021_A_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 2 0
## 6 1 1 1 1
## AX.93243024_C_C AX.93243024_C_HET AX.93243025_T_A AX.93243025_T_HET
## 1 0 0 1 1
## 2 1 1 1 1
## 3 0 0 1 1
## 4 1 1 1 1
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93243026_T_C AX.93243026_T_HET AX.93243027_T_C AX.93243027_T_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93243029_G_C AX.93243029_G_HET AX.93243031_A_C AX.93243031_A_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93243032_G_C AX.93243032_G_HET AX.93243036_A_C AX.93243036_A_HET
## 1 2 0 0 0
## 2 1 1 0 0
## 3 2 0 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93260772_A_C AX.93260772_A_HET AX.93260769_A_C AX.93260769_A_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93260767_A_C AX.93260767_A_HET AX.93260763_A_C AX.93260763_A_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 1 1 1 1
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93260758_C_C AX.93260758_C_HET AX.93249492_T_C AX.93249492_T_HET
## 1 0 0 0 0
## 2 0 0 2 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 2 0
## 6 0 0 2 0
## AX.93249494_C_C AX.93249494_C_HET AX.93249501_A_C AX.93249501_A_HET
## 1 1 1 1 1
## 2 1 1 0 0
## 3 1 1 1 1
## 4 1 1 0 0
## 5 1 1 0 0
## 6 2 0 0 0
## AX.93249503_T_C AX.93249503_T_HET AX.93249504_G_C AX.93249504_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93249506_G_C AX.93249506_G_HET AX.93249507_C_C AX.93249507_C_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93249509_C_A AX.93249509_C_HET AX.93249510_A_C AX.93249510_A_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 0 0 0 0
## 4 1 1 1 1
## 5 2 0 0 0
## 6 2 0 0 0
## AX.93249514_A_C AX.93249514_A_HET AX.93249515_T_C AX.93249515_T_HET
## 1 0 0 2 0
## 2 0 0 1 1
## 3 0 0 2 0
## 4 0 0 1 1
## 5 1 1 1 1
## 6 2 0 0 0
## AX.93249518_A_C AX.93249518_A_HET AX.93249519_T_C AX.93249519_T_HET
## 1 1 1 1 1
## 2 1 1 0 0
## 3 1 1 1 1
## 4 1 1 0 0
## 5 1 1 1 1
## 6 1 1 0 0
## AX.93216347_T_C AX.93216347_T_HET AX.93216344_G_C AX.93216344_G_HET
## 1 1 1 1 1
## 2 0 0 0 0
## 3 1 1 1 1
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93216342_C_C AX.93216342_C_HET AX.93231896_T_C AX.93231896_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93216338_T_C AX.93216338_T_HET AX.93216336_C_C AX.93216336_C_HET
## 1 0 0 1 1
## 2 1 1 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 2 0 1 1
## 6 2 0 2 0
## AX.93216335_T_C AX.93216335_T_HET AX.93216330_A_C AX.93216330_A_HET
## 1 0 0 2 0
## 2 0 0 0 0
## 3 0 0 2 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93216329_A_C AX.93216329_A_HET AX.93216327_T_C AX.93216327_T_HET
## 1 2 0 0 0
## 2 0 0 1 1
## 3 2 0 0 0
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93216326_A_C AX.93216326_A_HET AX.93216325_C_C AX.93216325_C_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 1 1
## 5 2 0 1 1
## 6 2 0 0 0
## AX.93216323_A_C AX.93216323_A_HET AX.93216322_C_C AX.93216322_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93216317_C_C AX.93216317_C_HET AX.93216315_T_C AX.93216315_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93216311_G_C AX.93216311_G_HET AX.93216310_T_C AX.93216310_T_HET
## 1 0 0 2 0
## 2 1 1 1 1
## 3 0 0 2 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 2 0 0 0
## AX.93216309_A_C AX.93216309_A_HET AX.93216308_T_C AX.93216308_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 2 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93216306_G_C AX.93216306_G_HET AX.93216305_C_C AX.93216305_C_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 2 0 0 0
## AX.93216303_C_C AX.93216303_C_HET AX.93216299_A_C AX.93216299_A_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 2 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93250521_G_C AX.93250521_G_HET AX.93250523_T_C AX.93250523_T_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 0 0 0 0
## 4 1 1 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93250525_G_C AX.93250525_G_HET AX.93250526_A_C AX.93250526_A_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93250529_T_C AX.93250529_T_HET AX.93250533_C_C AX.93250533_C_HET
## 1 1 1 1 1
## 2 0 0 1 1
## 3 1 1 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93250534_C_A AX.93250534_C_HET AX.93242907_C_0 AX.93242907_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 2 0 0 0
## 5 0 0 0 0
## 6 2 0 0 0
## AX.93242906_G_C AX.93242906_G_HET AX.93242905_G_0 AX.93242905_G_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93242903_T_C AX.93242903_T_HET AX.93242902_C_C AX.93242902_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93242901_C_C AX.93242901_C_HET AX.93242900_C_C AX.93242900_C_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93242897_C_C AX.93242897_C_HET AX.93242895_A_C AX.93242895_A_HET
## 1 1 1 1 1
## 2 0 0 1 1
## 3 1 1 1 1
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93242893_C_C AX.93242893_C_HET AX.93242889_A_C AX.93242889_A_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93242887_A_C AX.93242887_A_HET AX.93242881_C_C AX.93242881_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93242880_C_0 AX.93242880_C_HET AX.93242879_T_C AX.93242879_T_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93242878_A_C AX.93242878_A_HET AX.93242875_C_C AX.93242875_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93242873_T_C AX.93242873_T_HET AX.93242869_G_C AX.93242869_G_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93237117_G_C AX.93237117_G_HET AX.93237116_A_0 AX.93237116_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93237115_G_C AX.93237115_G_HET AX.93237114_A_0 AX.93237114_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93237113_A_C AX.93237113_A_HET AX.93237112_T_C AX.93237112_T_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93237110_G_C AX.93237110_G_HET AX.93237109_C_C AX.93237109_C_HET
## 1 1 1 1 1
## 2 0 0 1 1
## 3 1 1 1 1
## 4 1 1 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93237107_G_C AX.93237107_G_HET AX.93237102_C_C AX.93237102_C_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 0 0 0 0
## 4 1 1 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93237101_A_C AX.93237101_A_HET AX.93237097_G_C AX.93237097_G_HET
## 1 0 0 2 0
## 2 0 0 0 0
## 3 0 0 2 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93242858_G_C AX.93242858_G_HET AX.93237088_A_C AX.93237088_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93237087_T_C AX.93237087_T_HET AX.93237086_G_C AX.93237086_G_HET
## 1 1 1 0 0
## 2 0 0 1 1
## 3 1 1 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93237082_T_C AX.93237082_T_HET AX.93237080_G_C AX.93237080_G_HET
## 1 0 0 0 0
## 2 0 0 2 0
## 3 0 0 0 0
## 4 0 0 2 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93237076_T_C AX.93237076_T_HET AX.93237074_T_C AX.93237074_T_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 1 1 1 1
## AX.93251007_G_C AX.93251007_G_HET AX.93237073_T_C AX.93237073_T_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 0 0 2 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93237072_T_C AX.93237072_T_HET AX.93237070_T_C AX.93237070_T_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93237069_A_C AX.93237069_A_HET AX.93217363_C_A AX.93217363_C_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 1 1 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93240973_T_A AX.93240973_T_HET AX.93240974_A_C AX.93240974_A_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 2 0 0 0
## 5 2 0 1 1
## 6 0 0 0 0
## AX.93240979_T_C AX.93240979_T_HET AX.93240986_A_C AX.93240986_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 2 0
## 6 0 0 1 1
## AX.93240988_G_C AX.93240988_G_HET AX.93240989_G_C AX.93240989_G_HET
## 1 1 1 1 1
## 2 0 0 1 1
## 3 1 1 1 1
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93240993_A_C AX.93240993_A_HET AX.93240994_T_C AX.93240994_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 1 1
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93240995_A_A AX.93240995_A_HET AX.93240997_T_C AX.93240997_T_HET
## 1 2 0 1 1
## 2 0 0 1 1
## 3 2 0 1 1
## 4 0 0 1 1
## 5 0 0 1 1
## 6 1 1 1 1
## AX.93241000_C_C AX.93241000_C_HET AX.93241001_C_C AX.93241001_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 2 0 0 0
## 6 0 0 1 1
## AX.93241004_G_C AX.93241004_G_HET AX.93241005_A_C AX.93241005_A_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 2 0
## AX.93241006_A_C AX.93241006_A_HET AX.93241009_T_C AX.93241009_T_HET
## 1 0 0 1 1
## 2 1 1 2 0
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93241010_A_C AX.93241010_A_HET AX.93241011_C_C AX.93241011_C_HET
## 1 0 0 0 0
## 2 0 0 2 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93241014_G_C AX.93241014_G_HET AX.93241020_A_C AX.93241020_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93241021_C_C AX.93241021_C_HET AX.93241022_T_C AX.93241022_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93248846_C_C AX.93248846_C_HET AX.93248845_C_C AX.93248845_C_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93248840_G_C AX.93248840_G_HET AX.93248838_T_C AX.93248838_T_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93248837_A_C AX.93248837_A_HET AX.93248835_C_C AX.93248835_C_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 1 1 1 1
## 6 0 0 1 1
## AX.93248834_C_C AX.93248834_C_HET AX.93248831_T_C AX.93248831_T_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93248830_A_C AX.93248830_A_HET AX.93248829_A_C AX.93248829_A_HET
## 1 1 1 1 1
## 2 0 0 0 0
## 3 1 1 1 1
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93248828_T_C AX.93248828_T_HET AX.93248826_G_C AX.93248826_G_HET
## 1 0 0 1 1
## 2 2 0 2 0
## 3 0 0 1 1
## 4 2 0 2 0
## 5 0 0 0 0
## 6 1 1 1 1
## AX.93248825_T_C AX.93248825_T_HET AX.93248823_G_C AX.93248823_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 1 1
## 6 0 0 0 0
## AX.93248821_C_C AX.93248821_C_HET AX.93248819_A_C AX.93248819_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 1 1 0 0
## AX.93248812_A_C AX.93248812_A_HET AX.93248810_G_C AX.93248810_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 2 0 0 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93248809_G_C AX.93248809_G_HET AX.93248807_A_C AX.93248807_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 1 1
## AX.93248806_A_C AX.93248806_A_HET AX.93233940_C_C AX.93233940_C_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 1 1
## AX.93233937_C_C AX.93233937_C_HET AX.93233936_T_C AX.93233936_T_HET
## 1 2 0 2 0
## 2 2 0 2 0
## 3 2 0 2 0
## 4 0 0 2 0
## 5 2 0 0 0
## 6 2 0 0 0
## AX.93233935_C_C AX.93233935_C_HET AX.93233931_A_C AX.93233931_A_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 2 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93233929_G_C AX.93233929_G_HET AX.93233928_G_C AX.93233928_G_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93233926_G_C AX.93233926_G_HET AX.93233924_G_C AX.93233924_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93233923_A_C AX.93233923_A_HET AX.93233922_G_C AX.93233922_G_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93263224_A_C AX.93263224_A_HET AX.93215245_C_C AX.93215245_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93233920_A_C AX.93233920_A_HET AX.93233918_A_C AX.93233918_A_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 0 0 1 1
## 5 0 0 1 1
## 6 1 1 1 1
## AX.93233916_A_C AX.93233916_A_HET AX.93233915_G_C AX.93233915_G_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93233912_C_C AX.93233912_C_HET AX.93233911_G_A AX.93233911_G_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93233909_G_A AX.93233909_G_HET AX.93233906_C_C AX.93233906_C_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93233905_A_C AX.93233905_A_HET AX.93233903_A_C AX.93233903_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93254375_T_C AX.93254375_T_HET AX.93254374_T_C AX.93254374_T_HET
## 1 0 0 1 1
## 2 1 1 1 1
## 3 0 0 1 1
## 4 0 0 2 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93254373_T_C AX.93254373_T_HET AX.93254372_C_C AX.93254372_C_HET
## 1 1 1 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 2 0
## 5 1 1 2 0
## 6 2 0 0 0
## AX.93254370_G_C AX.93254370_G_HET AX.93254365_A_C AX.93254365_A_HET
## 1 1 1 1 1
## 2 1 1 0 0
## 3 1 1 1 1
## 4 2 0 0 0
## 5 1 1 0 0
## 6 0 0 1 1
## AX.93254362_G_C AX.93254362_G_HET AX.93254358_A_C AX.93254358_A_HET
## 1 1 1 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 0 0
## 5 2 0 2 0
## 6 1 1 2 0
## AX.93254355_G_C AX.93254355_G_HET AX.93254354_A_C AX.93254354_A_HET
## 1 0 0 1 1
## 2 0 0 NA NA
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93254352_G_C AX.93254352_G_HET AX.93254349_C_C AX.93254349_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93229826_C_C AX.93229826_C_HET AX.93254346_G_C AX.93254346_G_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93254345_A_C AX.93254345_A_HET AX.93254343_C_C AX.93254343_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93254342_A_C AX.93254342_A_HET AX.93254337_C_C AX.93254337_C_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 2 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93254336_A_C AX.93254336_A_HET AX.93254335_A_C AX.93254335_A_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93248245_A_C AX.93248245_A_HET AX.93258319_C_C AX.93258319_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93248243_A_C AX.93248243_A_HET AX.93248242_G_C AX.93248242_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93248241_C_C AX.93248241_C_HET AX.93248240_T_C AX.93248240_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93248239_C_C AX.93248239_C_HET AX.93248233_C_C AX.93248233_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93247466_T_C AX.93247466_T_HET AX.93247464_C_C AX.93247464_C_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93247460_G_C AX.93247460_G_HET AX.93260247_C_C AX.93260247_C_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93260249_T_C AX.93260249_T_HET AX.93257289_T_C AX.93257289_T_HET
## 1 1 1 0 0
## 2 NA NA 0 0
## 3 1 1 0 0
## 4 2 0 2 0
## 5 1 1 0 0
## 6 1 1 2 0
## AX.93257293_C_C AX.93257293_C_HET AX.93257294_G_C AX.93257294_G_HET
## 1 0 0 1 1
## 2 1 1 0 0
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93257295_C_C AX.93257295_C_HET AX.93257296_C_C AX.93257296_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93257297_T_C AX.93257297_T_HET AX.93257298_C_C AX.93257298_C_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 1 1 1 1
## 5 0 0 0 0
## 6 1 1 1 1
## AX.93257305_A_C AX.93257305_A_HET AX.93257306_G_A AX.93257306_G_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 1 1 2 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93257307_A_C AX.93257307_A_HET AX.93236102_A_C AX.93236102_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93236105_G_C AX.93236105_G_HET AX.93236106_G_C AX.93236106_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93236111_T_C AX.93236111_T_HET AX.93236112_A_A AX.93236112_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 2 0 2 0
## 5 2 0 2 0
## 6 1 1 2 0
## AX.93236114_A_C AX.93236114_A_HET AX.93236116_T_C AX.93236116_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93236117_T_C AX.93236117_T_HET AX.93236122_C_C AX.93236122_C_HET
## 1 0 0 2 0
## 2 0 0 2 0
## 3 0 0 2 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 2 0
## AX.93236124_G_C AX.93236124_G_HET AX.93236127_G_C AX.93236127_G_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 1 1 1 1
## AX.93236128_C_C AX.93236128_C_HET AX.93236129_T_C AX.93236129_T_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93228111_T_C AX.93228111_T_HET AX.93228113_C_C AX.93228113_C_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 2 0 1 1
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93228114_A_C AX.93228114_A_HET AX.93228117_G_C AX.93228117_G_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 0 0 2 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93228121_G_C AX.93228121_G_HET AX.93228123_A_C AX.93228123_A_HET
## 1 0 0 0 0
## 2 0 0 2 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 2 0
## AX.93228124_T_C AX.93228124_T_HET AX.93228129_A_C AX.93228129_A_HET
## 1 0 0 2 0
## 2 1 1 1 1
## 3 0 0 2 0
## 4 0 0 1 1
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93228130_C_C AX.93228130_C_HET AX.93228134_T_C AX.93228134_T_HET
## 1 1 1 1 1
## 2 1 1 2 0
## 3 1 1 1 1
## 4 0 0 0 0
## 5 1 1 2 0
## 6 1 1 2 0
## AX.93228135_A_A AX.93228135_A_HET AX.93228141_A_C AX.93228141_A_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93228142_C_C AX.93228142_C_HET AX.93228143_T_C AX.93228143_T_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93228144_G_C AX.93228144_G_HET AX.93260149_A_C AX.93260149_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93260147_G_C AX.93260147_G_HET AX.93260145_C_C AX.93260145_C_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93260142_C_C AX.93260142_C_HET AX.93260141_G_C AX.93260141_G_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93260140_A_C AX.93260140_A_HET AX.93260137_G_C AX.93260137_G_HET
## 1 2 0 0 0
## 2 1 1 2 0
## 3 2 0 0 0
## 4 1 1 0 0
## 5 1 1 2 0
## 6 1 1 0 0
## AX.93262226_A_C AX.93262226_A_HET AX.93257493_C_C AX.93257493_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93261214_A_C AX.93261214_A_HET AX.93261215_G_C AX.93261215_G_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93261216_G_C AX.93261216_G_HET AX.93261217_A_A AX.93261217_A_HET
## 1 2 0 1 1
## 2 0 0 2 0
## 3 2 0 1 1
## 4 0 0 2 0
## 5 0 0 1 1
## 6 1 1 1 1
## AX.93261220_A_C AX.93261220_A_HET AX.93238473_T_C AX.93238473_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93238475_G_C AX.93238475_G_HET AX.93238478_C_C AX.93238478_C_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 1 1 0 0
## 5 0 0 1 1
## 6 1 1 1 1
## AX.93238479_T_C AX.93238479_T_HET AX.93238480_C_C AX.93238480_C_HET
## 1 0 0 1 1
## 2 1 1 2 0
## 3 0 0 1 1
## 4 0 0 0 0
## 5 1 1 2 0
## 6 1 1 0 0
## AX.93238481_A_C AX.93238481_A_HET AX.93238482_G_C AX.93238482_G_HET
## 1 0 0 1 1
## 2 1 1 0 0
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93233042_T_C AX.93233042_T_HET AX.93233041_G_C AX.93233041_G_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 0 0 1 1
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93233037_C_C AX.93233037_C_HET AX.93233036_C_C AX.93233036_C_HET
## 1 0 0 2 0
## 2 0 0 2 0
## 3 0 0 2 0
## 4 0 0 0 0
## 5 1 1 2 0
## 6 0 0 0 0
## AX.93233031_T_C AX.93233031_T_HET AX.93233029_C_C AX.93233029_C_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 1 1 1 1
## AX.93233026_A_C AX.93233026_A_HET AX.93244396_G_C AX.93244396_G_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 2 0 0 0
## 5 1 1 1 1
## 6 2 0 1 1
## AX.93244394_G_C AX.93244394_G_HET AX.93244391_A_A AX.93244391_A_HET
## 1 0 0 1 1
## 2 1 1 2 0
## 3 0 0 1 1
## 4 1 1 1 1
## 5 1 1 1 1
## 6 1 1 1 1
## AX.93244387_C_C AX.93244387_C_HET AX.93244386_A_C AX.93244386_A_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 0 0 0 0
## 4 1 1 1 1
## 5 0 0 0 0
## 6 1 1 1 1
## AX.93263727_T_C AX.93263727_T_HET AX.93261068_T_C AX.93261068_T_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93261070_C_C AX.93261070_C_HET AX.93261071_A_C AX.93261071_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93258677_C_C AX.93258677_C_HET AX.93258671_A_C AX.93258671_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93258670_G_C AX.93258670_G_HET AX.93258669_T_C AX.93258669_T_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93258667_G_C AX.93258667_G_HET AX.93258666_G_C AX.93258666_G_HET
## 1 0 0 2 0
## 2 0 0 0 0
## 3 0 0 2 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93255381_A_C AX.93255381_A_HET AX.93217758_C_A AX.93217758_C_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 2 0
## AX.93217760_A_C AX.93217760_A_HET AX.93217761_G_C AX.93217761_G_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93217763_T_C AX.93217763_T_HET AX.93217764_G_C AX.93217764_G_HET
## 1 0 0 0 0
## 2 2 0 1 1
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93217767_A_C AX.93217767_A_HET AX.93217768_T_C AX.93217768_T_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 2 0
## 4 0 0 1 1
## 5 0 0 1 1
## 6 1 1 0 0
## AX.93217769_T_C AX.93217769_T_HET AX.93217771_G_C AX.93217771_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93217772_G_C AX.93217772_G_HET AX.93217773_G_C AX.93217773_G_HET
## 1 0 0 2 0
## 2 2 0 1 1
## 3 1 1 1 1
## 4 1 1 1 1
## 5 1 1 0 0
## 6 1 1 1 1
## AX.93221584_T_C AX.93221584_T_HET AX.93260652_A_C AX.93260652_A_HET
## 1 0 0 0 0
## 2 1 1 2 0
## 3 0 0 0 0
## 4 0 0 2 0
## 5 0 0 2 0
## 6 0 0 2 0
## AX.93260653_T_C AX.93260653_T_HET AX.93260654_T_C AX.93260654_T_HET
## 1 0 0 1 1
## 2 2 0 1 1
## 3 0 0 0 0
## 4 2 0 1 1
## 5 2 0 1 1
## 6 2 0 0 0
## AX.93260655_T_C AX.93260655_T_HET AX.93260656_C_C AX.93260656_C_HET
## 1 0 0 1 1
## 2 0 0 2 0
## 3 0 0 NA NA
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93260659_G_C AX.93260659_G_HET AX.93245477_G_C AX.93245477_G_HET
## 1 1 1 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93245476_G_C AX.93245476_G_HET AX.93245473_G_C AX.93245473_G_HET
## 1 0 0 2 0
## 2 0 0 0 0
## 3 0 0 1 1
## 4 0 0 0 0
## 5 2 0 1 1
## 6 1 1 2 0
## AX.93245472_G_C AX.93245472_G_HET AX.93245469_C_C AX.93245469_C_HET
## 1 1 1 2 0
## 2 0 0 2 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 2 0
## AX.93245467_A_C AX.93245467_A_HET AX.93245466_A_C AX.93245466_A_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 2 0 0 0
## 5 2 0 0 0
## 6 0 0 1 1
## AX.93245465_G_C AX.93245465_G_HET AX.93245464_T_C AX.93245464_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93245462_C_C AX.93245462_C_HET AX.93245460_T_C AX.93245460_T_HET
## 1 0 0 0 0
## 2 2 0 1 1
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93245458_A_C AX.93245458_A_HET AX.93245456_A_C AX.93245456_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93245449_G_C AX.93245449_G_HET AX.93235477_T_C AX.93235477_T_HET
## 1 1 1 1 1
## 2 1 1 2 0
## 3 0 0 2 0
## 4 0 0 1 1
## 5 0 0 1 1
## 6 1 1 0 0
## AX.93235481_A_C AX.93235481_A_HET AX.93235482_T_C AX.93235482_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93235485_C_A AX.93235485_C_HET AX.93235487_A_C AX.93235487_A_HET
## 1 2 0 2 0
## 2 1 1 0 0
## 3 2 0 1 1
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93235488_C_C AX.93235488_C_HET AX.93235490_A_C AX.93235490_A_HET
## 1 0 0 2 0
## 2 0 0 0 0
## 3 0 0 1 1
## 4 1 1 0 0
## 5 0 0 0 0
## 6 2 0 0 0
## AX.93235494_A_C AX.93235494_A_HET AX.93235496_A_A AX.93235496_A_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 2 0
## AX.93259015_A_C AX.93259015_A_HET AX.93259021_C_C AX.93259021_C_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 2 0 0 0
## 5 1 1 0 0
## 6 2 0 0 0
## AX.93259022_T_C AX.93259022_T_HET AX.93232978_G_C AX.93232978_G_HET
## 1 2 0 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 1 1 1 1
## 5 0 0 0 0
## 6 2 0 0 0
## AX.93232979_C_C AX.93232979_C_HET AX.93232981_C_C AX.93232981_C_HET
## 1 0 0 2 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 2 0
## 6 0 0 0 0
## AX.93232982_A_C AX.93232982_A_HET AX.93232984_C_C AX.93232984_C_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 0 0 1 1
## 4 2 0 0 0
## 5 2 0 0 0
## 6 1 1 1 1
## AX.93232986_G_C AX.93232986_G_HET AX.93232989_G_C AX.93232989_G_HET
## 1 1 1 0 0
## 2 0 0 2 0
## 3 1 1 0 0
## 4 1 1 NA NA
## 5 0 0 1 1
## 6 2 0 2 0
## AX.93232990_C_C AX.93232990_C_HET AX.93232991_A_C AX.93232991_A_HET
## 1 1 1 1 1
## 2 0 0 0 0
## 3 0 0 1 1
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93232992_A_C AX.93232992_A_HET AX.93232993_T_C AX.93232993_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 1 1 1 1
## AX.93232997_C_C AX.93232997_C_HET AX.93262770_T_C AX.93262770_T_HET
## 1 2 0 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93248345_C_C AX.93248345_C_HET AX.93248341_T_C AX.93248341_T_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93248338_C_C AX.93248338_C_HET AX.93248337_T_C AX.93248337_T_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 0 0 1 1
## 6 1 1 0 0
## AX.93248335_G_C AX.93248335_G_HET AX.93248334_C_C AX.93248334_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 1 1 0 0
## AX.93248332_G_C AX.93248332_G_HET AX.93254739_C_C AX.93254739_C_HET
## 1 0 0 0 0
## 2 0 0 2 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93254738_C_C AX.93254738_C_HET AX.93254736_C_C AX.93254736_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93254734_A_C AX.93254734_A_HET AX.93254733_C_C AX.93254733_C_HET
## 1 0 0 1 1
## 2 1 1 0 0
## 3 0 0 2 0
## 4 0 0 2 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93254732_G_C AX.93254732_G_HET AX.93254729_T_C AX.93254729_T_HET
## 1 1 1 0 0
## 2 2 0 0 0
## 3 1 1 0 0
## 4 0 0 1 1
## 5 2 0 0 0
## 6 0 0 0 0
## AX.93254728_A_C AX.93254728_A_HET AX.93254724_G_C AX.93254724_G_HET
## 1 0 0 0 0
## 2 0 0 2 0
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93248109_A_C AX.93248109_A_HET AX.93248110_C_C AX.93248110_C_HET
## 1 0 0 1 1
## 2 1 1 1 1
## 3 0 0 2 0
## 4 2 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93248115_G_C AX.93248115_G_HET AX.93248116_T_C AX.93248116_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93248117_A_C AX.93248117_A_HET AX.93252543_G_C AX.93252543_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93252545_G_C AX.93252545_G_HET AX.93252553_A_C AX.93252553_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93252554_G_C AX.93252554_G_HET AX.93218615_A_C AX.93218615_A_HET
## 1 0 0 2 0
## 2 0 0 2 0
## 3 0 0 1 1
## 4 0 0 1 1
## 5 1 1 NA NA
## 6 0 0 0 0
## AX.93252556_G_C AX.93252556_G_HET AX.93252568_A_C AX.93252568_A_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93252569_A_C AX.93252569_A_HET AX.93252571_C_C AX.93252571_C_HET
## 1 0 0 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 1 1 1 1
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93249957_A_C AX.93249957_A_HET AX.93249959_A_C AX.93249959_A_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93224897_A_C AX.93224897_A_HET AX.93224905_A_C AX.93224905_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93224907_T_C AX.93224907_T_HET AX.93224908_G_C AX.93224908_G_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 2 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93224909_G_C AX.93224909_G_HET AX.93225346_G_A AX.93225346_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 2 0
## 5 0 0 0 0
## 6 0 0 2 0
## AX.93224918_C_C AX.93224918_C_HET AX.93224919_A_C AX.93224919_A_HET
## 1 0 0 0 0
## 2 2 0 0 0
## 3 0 0 0 0
## 4 2 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93224926_C_C AX.93224926_C_HET AX.93261948_A_C AX.93261948_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93261949_G_C AX.93261949_G_HET AX.93261952_C_C AX.93261952_C_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93243726_T_C AX.93243726_T_HET AX.93243723_A_C AX.93243723_A_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93243721_T_C AX.93243721_T_HET AX.93243720_A_C AX.93243720_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93243719_G_C AX.93243719_G_HET AX.93243714_C_C AX.93243714_C_HET
## 1 1 1 0 0
## 2 2 0 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93243708_T_C AX.93243708_T_HET AX.93243707_A_C AX.93243707_A_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 2 0
## 6 0 0 0 0
## AX.93243706_A_C AX.93243706_A_HET AX.93243704_T_C AX.93243704_T_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 2 0
## 6 0 0 0 0
## AX.93243701_G_C AX.93243701_G_HET AX.93243699_G_C AX.93243699_G_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 0 0 0 0
## 4 0 0 0 0
## 5 2 0 1 1
## 6 0 0 0 0
## AX.93243697_A_C AX.93243697_A_HET AX.93243695_T_0 AX.93243695_T_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 1 1 0 0
## 4 2 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93243694_T_0 AX.93243694_T_HET AX.93243693_T_0 AX.93243693_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93243692_A_C AX.93243692_A_HET AX.93243691_A_0 AX.93243691_A_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 2 0 0 0
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93243690_T_C AX.93243690_T_HET AX.93243689_A_0 AX.93243689_A_HET
## 1 0 0 0 0
## 2 2 0 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93257776_A_C AX.93257776_A_HET AX.93257777_T_C AX.93257777_T_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93257780_T_C AX.93257780_T_HET AX.93257781_T_C AX.93257781_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 1 1 1 1
## 6 0 0 1 1
## AX.93257359_A_C AX.93257359_A_HET AX.93257360_T_C AX.93257360_T_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 1 1 2 0
## 4 1 1 2 0
## 5 0 0 0 0
## 6 1 1 2 0
## AX.93257361_T_C AX.93257361_T_HET AX.93257363_C_C AX.93257363_C_HET
## 1 1 1 2 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 1 1 2 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93257364_G_C AX.93257364_G_HET AX.93257365_T_C AX.93257365_T_HET
## 1 0 0 1 1
## 2 1 1 1 1
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93257366_C_C AX.93257366_C_HET AX.93246079_A_C AX.93246079_A_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 2 0 0 0
## 4 1 1 1 1
## 5 0 0 0 0
## 6 1 1 2 0
## AX.93246082_C_C AX.93246082_C_HET AX.93246083_G_C AX.93246083_G_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93246084_T_C AX.93246084_T_HET AX.93246086_C_C AX.93246086_C_HET
## 1 1 1 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 1 1 1 1
## 5 1 1 1 1
## 6 1 1 0 0
## AX.93246087_G_C AX.93246087_G_HET AX.93246089_G_C AX.93246089_G_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 2 0 0 0
## AX.93246090_T_C AX.93246090_T_HET AX.93246091_A_C AX.93246091_A_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93246093_A_C AX.93246093_A_HET AX.93246094_A_C AX.93246094_A_HET
## 1 0 0 0 0
## 2 2 0 1 1
## 3 1 1 1 1
## 4 1 1 0 0
## 5 0 0 0 0
## 6 1 1 1 1
## AX.93246095_T_C AX.93246095_T_HET AX.93246097_G_C AX.93246097_G_HET
## 1 0 0 1 1
## 2 2 0 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 2 0 0 0
## AX.93259155_A_C AX.93259155_A_HET AX.93259157_G_C AX.93259157_G_HET
## 1 2 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 2 0
## 6 0 0 0 0
## AX.93259159_C_C AX.93259159_C_HET AX.93259162_T_C AX.93259162_T_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 1 1
## AX.93259163_T_C AX.93259163_T_HET AX.93259164_A_C AX.93259164_A_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 1 1
## 6 1 1 0 0
## AX.93259165_T_C AX.93259165_T_HET AX.93259166_T_C AX.93259166_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 2 0
## 6 1 1 0 0
## AX.93261797_C_C AX.93261797_C_HET AX.93261799_T_0 AX.93261799_T_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 2 0 0 0
## 6 1 1 0 0
## AX.93261801_A_C AX.93261801_A_HET AX.93261802_G_C AX.93261802_G_HET
## 1 1 1 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 0 0
## 5 1 1 1 1
## 6 0 0 0 0
## AX.93261803_A_C AX.93261803_A_HET AX.93261804_A_C AX.93261804_A_HET
## 1 1 1 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 0 0
## 5 1 1 1 1
## 6 0 0 0 0
## AX.93237318_G_C AX.93237318_G_HET AX.93237317_C_C AX.93237317_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 1 1 1 1
## 6 0 0 0 0
## AX.93237316_T_C AX.93237316_T_HET AX.93237314_G_C AX.93237314_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93237313_C_C AX.93237313_C_HET AX.93237312_T_C AX.93237312_T_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 1 1 1 1
## 6 0 0 1 1
## AX.93237311_C_C AX.93237311_C_HET AX.93237307_T_C AX.93237307_T_HET
## 1 2 0 0 0
## 2 1 1 1 1
## 3 1 1 1 1
## 4 1 1 1 1
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93255299_A_C AX.93255299_A_HET AX.93255301_G_C AX.93255301_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93255302_T_C AX.93255302_T_HET AX.93255304_T_C AX.93255304_T_HET
## 1 1 1 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 2 0 0 0
## 5 1 1 1 1
## 6 0 0 1 1
## AX.93255305_G_C AX.93255305_G_HET AX.93246077_A_C AX.93246077_A_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93246074_T_C AX.93246074_T_HET AX.93246069_A_C AX.93246069_A_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93246068_G_C AX.93246068_G_HET AX.93256536_C_C AX.93256536_C_HET
## 1 0 0 2 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93256535_G_C AX.93256535_G_HET AX.93252080_T_C AX.93252080_T_HET
## 1 NA NA 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93252078_T_C AX.93252078_T_HET AX.93252076_A_C AX.93252076_A_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 2 0
## AX.93252075_A_C AX.93252075_A_HET AX.93219077_C_C AX.93219077_C_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 2 0
## AX.93219078_T_C AX.93219078_T_HET AX.93219079_A_C AX.93219079_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93219080_T_C AX.93219080_T_HET AX.93219081_C_C AX.93219081_C_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93219085_G_C AX.93219085_G_HET AX.93219087_C_C AX.93219087_C_HET
## 1 1 1 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 1 1 1 1
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93219088_A_C AX.93219088_A_HET AX.93219089_G_C AX.93219089_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93219091_T_C AX.93219091_T_HET AX.93219093_T_C AX.93219093_T_HET
## 1 0 0 NA NA
## 2 1 1 2 0
## 3 1 1 2 0
## 4 1 1 0 0
## 5 1 1 1 1
## 6 1 1 1 1
## AX.93219094_A_C AX.93219094_A_HET AX.93219098_T_C AX.93219098_T_HET
## 1 1 1 0 0
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93219101_A_C AX.93219101_A_HET AX.93219104_T_C AX.93219104_T_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93219105_A_C AX.93219105_A_HET AX.93246309_T_C AX.93246309_T_HET
## 1 1 1 1 1
## 2 2 0 1 1
## 3 2 0 1 1
## 4 1 1 0 0
## 5 1 1 0 0
## 6 2 0 0 0
## AX.93219110_G_C AX.93219110_G_HET AX.93219112_G_C AX.93219112_G_HET
## 1 1 1 0 0
## 2 2 0 1 1
## 3 2 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 1 1 0 0
## AX.93219114_C_C AX.93219114_C_HET AX.93219115_A_C AX.93219115_A_HET
## 1 2 0 1 1
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93219121_T_A AX.93219121_T_HET AX.93219125_C_A AX.93219125_C_HET
## 1 2 0 2 0
## 2 2 0 2 0
## 3 2 0 2 0
## 4 1 1 1 1
## 5 2 0 2 0
## 6 2 0 2 0
## AX.93219126_C_C AX.93219126_C_HET AX.93219127_C_A AX.93219127_C_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 1 1
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93219128_A_C AX.93219128_A_HET AX.93219130_C_0 AX.93219130_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93219131_G_C AX.93219131_G_HET AX.93219137_T_C AX.93219137_T_HET
## 1 2 0 0 0
## 2 2 0 0 0
## 3 2 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93219141_T_C AX.93219141_T_HET AX.93219142_A_C AX.93219142_A_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93219145_C_C AX.93219145_C_HET AX.93219148_T_C AX.93219148_T_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 2 0 0 0
## AX.93219153_T_C AX.93219153_T_HET AX.93219155_G_C AX.93219155_G_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93260951_G_C AX.93260951_G_HET AX.93260955_C_C AX.93260955_C_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 1 1 1 1
## 5 0 0 1 1
## 6 0 0 2 0
## AX.93245796_A_C AX.93245796_A_HET AX.93245799_T_C AX.93245799_T_HET
## 1 1 1 2 0
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93245802_T_C AX.93245802_T_HET AX.93245804_C_C AX.93245804_C_HET
## 1 1 1 2 0
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 1 1
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93245808_T_C AX.93245808_T_HET AX.93245809_T_C AX.93245809_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 2 0
## 5 0 0 1 1
## 6 1 1 1 1
## AX.93229569_T_C AX.93229569_T_HET AX.93233586_T_C AX.93233586_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93229570_G_C AX.93229570_G_HET AX.93229571_G_C AX.93229571_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 2 0 1 1
## AX.93252828_A_C AX.93252828_A_HET AX.93252829_G_C AX.93252829_G_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93251553_T_C AX.93251553_T_HET AX.93251555_G_A AX.93251555_G_HET
## 1 0 0 1 1
## 2 0 0 2 0
## 3 0 0 2 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 2 0
## AX.93251557_A_C AX.93251557_A_HET AX.93251558_A_C AX.93251558_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93251560_G_C AX.93251560_G_HET AX.93251561_C_C AX.93251561_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93251567_T_C AX.93251567_T_HET AX.93251568_A_C AX.93251568_A_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93251569_A_C AX.93251569_A_HET AX.93251572_C_C AX.93251572_C_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93251576_T_C AX.93251576_T_HET AX.93251577_A_C AX.93251577_A_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93251581_G_C AX.93251581_G_HET AX.93251582_A_C AX.93251582_A_HET
## 1 1 1 1 1
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 1 1
## 5 1 1 0 0
## 6 1 1 NA NA
## AX.93248006_T_C AX.93248006_T_HET AX.93248004_G_C AX.93248004_G_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 1 1
## AX.93248002_A_C AX.93248002_A_HET AX.93248001_G_C AX.93248001_G_HET
## 1 0 0 1 1
## 2 0 0 2 0
## 3 0 0 2 0
## 4 0 0 1 1
## 5 0 0 2 0
## 6 0 0 1 1
## AX.93248000_C_C AX.93248000_C_HET AX.93247999_C_C AX.93247999_C_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93247997_A_C AX.93247997_A_HET AX.93256178_T_C AX.93256178_T_HET
## 1 1 1 NA NA
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93256177_G_C AX.93256177_G_HET AX.93256176_A_C AX.93256176_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93256172_A_C AX.93256172_A_HET AX.93256171_C_C AX.93256171_C_HET
## 1 2 0 0 0
## 2 2 0 0 0
## 3 2 0 0 0
## 4 0 0 1 1
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93256169_A_C AX.93256169_A_HET AX.93256168_C_A AX.93256168_C_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 1 1 1 1
## 5 0 0 2 0
## 6 1 1 1 1
## AX.93256166_T_C AX.93256166_T_HET AX.93256165_C_C AX.93256165_C_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93256163_T_C AX.93256163_T_HET AX.93256161_G_C AX.93256161_G_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93256159_A_C AX.93256159_A_HET AX.93256158_G_C AX.93256158_G_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93243086_G_C AX.93243086_G_HET AX.93257424_T_C AX.93257424_T_HET
## 1 1 1 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 2 0 2 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93257422_G_C AX.93257422_G_HET AX.93217945_G_C AX.93217945_G_HET
## 1 2 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 2 0 1 1
## 5 1 1 0 0
## 6 2 0 0 0
## AX.93217944_G_C AX.93217944_G_HET AX.93217943_A_C AX.93217943_A_HET
## 1 1 1 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 1 1 0 0
## 5 0 0 0 0
## 6 1 1 2 0
## AX.93217942_A_A AX.93217942_A_HET AX.93217941_G_C AX.93217941_G_HET
## 1 2 0 0 0
## 2 2 0 0 0
## 3 2 0 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 2 0 1 1
## AX.93217938_G_C AX.93217938_G_HET AX.93217937_A_C AX.93217937_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 2 0
## AX.93217933_T_C AX.93217933_T_HET AX.93217932_G_C AX.93217932_G_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93217930_G_C AX.93217930_G_HET AX.93217929_A_C AX.93217929_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93217928_A_C AX.93217928_A_HET AX.93263625_T_C AX.93263625_T_HET
## 1 1 1 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 1 1 1 1
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93217927_A_C AX.93217927_A_HET AX.93217925_A_C AX.93217925_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 1 1 1 1
## 6 0 0 1 1
## AX.93217924_A_A AX.93217924_A_HET AX.93217917_C_C AX.93217917_C_HET
## 1 1 1 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 1 1 0 0
## 5 0 0 1 1
## 6 0 0 2 0
## AX.93217915_G_C AX.93217915_G_HET AX.93217914_G_C AX.93217914_G_HET
## 1 0 0 1 1
## 2 1 1 0 0
## 3 1 1 0 0
## 4 2 0 2 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93217910_T_C AX.93217910_T_HET AX.93217908_T_C AX.93217908_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 1 1 1 1
## 6 0 0 2 0
## AX.93217907_G_C AX.93217907_G_HET AX.93217905_A_C AX.93217905_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 1 1
## 6 2 0 2 0
## AX.93217903_C_C AX.93217903_C_HET AX.93217901_G_C AX.93217901_G_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 1 1
## 6 2 0 2 0
## AX.93217900_T_C AX.93217900_T_HET AX.93217894_C_C AX.93217894_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93217892_T_C AX.93217892_T_HET AX.93217891_G_C AX.93217891_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 2 0 0 0
## AX.93217890_T_C AX.93217890_T_HET AX.93217885_C_C AX.93217885_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 2 0 0 0
## AX.93217882_G_C AX.93217882_G_HET AX.93217881_G_C AX.93217881_G_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93217872_C_C AX.93217872_C_HET AX.93217866_A_C AX.93217866_A_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93217862_C_C AX.93217862_C_HET AX.93217860_G_C AX.93217860_G_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 2 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93217858_C_C AX.93217858_C_HET AX.93217857_T_C AX.93217857_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93217853_T_C AX.93217853_T_HET AX.93217852_G_C AX.93217852_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93217851_T_C AX.93217851_T_HET AX.93217850_G_C AX.93217850_G_HET
## 1 0 0 1 1
## 2 0 0 2 0
## 3 0 0 2 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93217849_T_C AX.93217849_T_HET AX.93217843_C_C AX.93217843_C_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93217842_A_C AX.93217842_A_HET AX.93217841_G_C AX.93217841_G_HET
## 1 0 0 0 0
## 2 2 0 0 0
## 3 2 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 2 0 1 1
## AX.93217839_C_C AX.93217839_C_HET AX.93217832_C_C AX.93217832_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93217830_T_C AX.93217830_T_HET AX.93217828_T_C AX.93217828_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93217822_T_C AX.93217822_T_HET AX.93260751_C_C AX.93260751_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 2 0 1 1
## 5 1 1 0 0
## 6 2 0 0 0
## AX.93260752_G_C AX.93260752_G_HET AX.93260753_G_A AX.93260753_G_HET
## 1 0 0 1 1
## 2 0 0 2 0
## 3 0 0 2 0
## 4 1 1 2 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93260755_C_A AX.93260755_C_HET AX.93252036_T_C AX.93252036_T_HET
## 1 2 0 1 1
## 2 2 0 0 0
## 3 2 0 0 0
## 4 2 0 0 0
## 5 2 0 0 0
## 6 2 0 1 1
## AX.93252034_G_C AX.93252034_G_HET AX.93252030_G_C AX.93252030_G_HET
## 1 1 1 2 0
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93252029_C_C AX.93252029_C_HET AX.93252027_G_C AX.93252027_G_HET
## 1 1 1 2 0
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 2 0
## AX.93233437_A_C AX.93233437_A_HET AX.93233438_G_C AX.93233438_G_HET
## 1 0 0 1 1
## 2 1 1 2 0
## 3 1 1 2 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93233442_A_C AX.93233442_A_HET AX.93233443_C_C AX.93233443_C_HET
## 1 1 1 0 0
## 2 2 0 0 0
## 3 2 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 2 0
## AX.93233445_C_C AX.93233445_C_HET AX.93233446_G_C AX.93233446_G_HET
## 1 1 1 0 0
## 2 2 0 0 0
## 3 2 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93233448_T_C AX.93233448_T_HET AX.93233449_G_C AX.93233449_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93233450_A_C AX.93233450_A_HET AX.93233452_A_C AX.93233452_A_HET
## 1 0 0 1 1
## 2 0 0 2 0
## 3 0 0 2 0
## 4 0 0 1 1
## 5 0 0 1 1
## 6 0 0 2 0
## AX.93233455_A_C AX.93233455_A_HET AX.93233457_G_C AX.93233457_G_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 1 1 1 1
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93233458_T_C AX.93233458_T_HET AX.93233459_G_C AX.93233459_G_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93233460_C_C AX.93233460_C_HET AX.93233462_G_C AX.93233462_G_HET
## 1 1 1 1 1
## 2 2 0 0 0
## 3 2 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93233466_T_C AX.93233466_T_HET AX.93233467_T_C AX.93233467_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 1 1
## 5 1 1 1 1
## 6 1 1 1 1
## AX.93233470_A_C AX.93233470_A_HET AX.93233473_C_C AX.93233473_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93233474_T_C AX.93233474_T_HET AX.93233477_C_C AX.93233477_C_HET
## 1 2 0 0 0
## 2 1 1 1 1
## 3 1 1 1 1
## 4 1 1 1 1
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93233478_T_C AX.93233478_T_HET AX.93233479_G_C AX.93233479_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93233482_T_C AX.93233482_T_HET AX.93233483_G_C AX.93233483_G_HET
## 1 1 1 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93233484_C_C AX.93233484_C_HET AX.93233487_C_C AX.93233487_C_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 2 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93233488_A_C AX.93233488_A_HET AX.93233489_G_C AX.93233489_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93233494_T_C AX.93233494_T_HET AX.93233497_A_C AX.93233497_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 1 1
## 5 0 0 1 1
## 6 1 1 1 1
## AX.93233500_C_C AX.93233500_C_HET AX.93242297_C_C AX.93242297_C_HET
## 1 1 1 1 1
## 2 2 0 1 1
## 3 2 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93242299_C_C AX.93242299_C_HET AX.93246035_T_C AX.93246035_T_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93242305_C_C AX.93242305_C_HET AX.93242308_C_C AX.93242308_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93242311_C_C AX.93242311_C_HET AX.93242313_C_C AX.93242313_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93250183_G_C AX.93250183_G_HET AX.93250182_C_C AX.93250182_C_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 1 1 0 0
## AX.93250180_A_C AX.93250180_A_HET AX.93250177_G_C AX.93250177_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93250176_T_C AX.93250176_T_HET AX.93250172_C_C AX.93250172_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 1 1
## 6 0 0 2 0
## AX.93250165_A_C AX.93250165_A_HET AX.93250163_G_C AX.93250163_G_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93250162_C_C AX.93250162_C_HET AX.93250160_C_C AX.93250160_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93250157_T_C AX.93250157_T_HET AX.93236165_G_C AX.93236165_G_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 2 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93236166_C_C AX.93236166_C_HET AX.93236167_A_C AX.93236167_A_HET
## 1 2 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 2 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93236168_G_C AX.93236168_G_HET AX.93236169_G_C AX.93236169_G_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93236170_T_C AX.93236170_T_HET AX.93236175_C_C AX.93236175_C_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 1 1
## 6 0 0 0 0
## AX.93236177_G_C AX.93236177_G_HET AX.93236178_C_C AX.93236178_C_HET
## 1 1 1 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 0 0
## 5 2 0 1 1
## 6 0 0 0 0
## AX.93236179_C_C AX.93236179_C_HET AX.93236182_C_C AX.93236182_C_HET
## 1 1 1 2 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 2 0 1 1
## AX.93236183_G_C AX.93236183_G_HET AX.93236185_C_C AX.93236185_C_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93236187_T_C AX.93236187_T_HET AX.93236188_C_C AX.93236188_C_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93236190_T_C AX.93236190_T_HET AX.93236192_T_C AX.93236192_T_HET
## 1 1 1 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93236195_T_C AX.93236195_T_HET AX.93236196_A_C AX.93236196_A_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 0 0
## 4 NA NA 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93236198_C_C AX.93236198_C_HET AX.93236205_T_C AX.93236205_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93236208_C_C AX.93236208_C_HET AX.93236209_G_C AX.93236209_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 1 1 1 1
## 6 0 0 1 1
## AX.93236214_T_C AX.93236214_T_HET AX.93236218_A_C AX.93236218_A_HET
## 1 2 0 0 0
## 2 1 1 1 1
## 3 1 1 1 1
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93236219_T_C AX.93236219_T_HET AX.93262061_T_C AX.93262061_T_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 2 0
## AX.93262062_C_C AX.93262062_C_HET AX.93262064_A_C AX.93262064_A_HET
## 1 2 0 1 1
## 2 2 0 1 1
## 3 2 0 1 1
## 4 0 0 0 0
## 5 2 0 1 1
## 6 2 0 1 1
## AX.93262065_T_C AX.93262065_T_HET AX.93262066_A_C AX.93262066_A_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 1 1 0 0
## 5 0 0 2 0
## 6 0 0 1 1
## AX.93262069_C_C AX.93262069_C_HET AX.93262070_T_C AX.93262070_T_HET
## 1 1 1 1 1
## 2 2 0 2 0
## 3 2 0 2 0
## 4 1 1 1 1
## 5 0 0 0 0
## 6 2 0 2 0
## AX.93262071_G_C AX.93262071_G_HET AX.93262074_A_C AX.93262074_A_HET
## 1 1 1 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 1 1
## 5 1 1 1 1
## 6 0 0 0 0
## AX.93261307_C_C AX.93261307_C_HET AX.93261308_A_C AX.93261308_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 NA NA
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93261309_A_C AX.93261309_A_HET AX.93261315_G_C AX.93261315_G_HET
## 1 1 1 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 2 0
## 6 0 0 1 1
## AX.93261316_C_C AX.93261316_C_HET AX.93261317_C_C AX.93261317_C_HET
## 1 1 1 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 2 0
## 5 0 0 0 0
## 6 0 0 NA NA
## AX.93227320_G_C AX.93227320_G_HET AX.93227322_A_C AX.93227322_A_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 2 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93227332_T_C AX.93227332_T_HET AX.93227334_A_C AX.93227334_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93227336_A_C AX.93227336_A_HET AX.93227337_G_C AX.93227337_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 1 1
## 6 0 0 0 0
## AX.93227339_A_C AX.93227339_A_HET AX.93227340_T_C AX.93227340_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93227341_T_C AX.93227341_T_HET AX.93227343_T_C AX.93227343_T_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93227345_A_C AX.93227345_A_HET AX.93227348_A_A AX.93227348_A_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 2 0
## 6 0 0 2 0
## AX.93227350_A_C AX.93227350_A_HET AX.93227351_C_C AX.93227351_C_HET
## 1 0 0 1 1
## 2 1 1 2 0
## 3 1 1 2 0
## 4 1 1 1 1
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93227352_C_C AX.93227352_C_HET AX.93227354_A_C AX.93227354_A_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93227362_T_C AX.93227362_T_HET AX.93227363_C_C AX.93227363_C_HET
## 1 1 1 1 1
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93227364_G_C AX.93227364_G_HET AX.93227366_A_C AX.93227366_A_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 1 1 2 0
## 5 1 1 1 1
## 6 1 1 2 0
## AX.93227370_G_C AX.93227370_G_HET AX.93227371_G_C AX.93227371_G_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 1 1
## 5 0 0 2 0
## 6 0 0 2 0
## AX.93227372_C_C AX.93227372_C_HET AX.93227374_G_C AX.93227374_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93227376_A_C AX.93227376_A_HET AX.93227378_A_C AX.93227378_A_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 2 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93227379_G_C AX.93227379_G_HET AX.93223555_T_C AX.93223555_T_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 2 0 1 1
## AX.93223553_T_C AX.93223553_T_HET AX.93223548_G_A AX.93223548_G_HET
## 1 1 1 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 2 0
## 5 1 1 2 0
## 6 1 1 1 1
## AX.93252818_A_C AX.93252818_A_HET AX.93252817_A_0 AX.93252817_A_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 2 0 0 0
## 6 0 0 0 0
## AX.93252816_A_A AX.93252816_A_HET AX.93252814_T_C AX.93252814_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 1 1
## AX.93252812_A_C AX.93252812_A_HET AX.93252811_A_C AX.93252811_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93252807_A_C AX.93252807_A_HET AX.93252806_C_C AX.93252806_C_HET
## 1 0 0 2 0
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 1 1
## AX.93252804_A_C AX.93252804_A_HET AX.93252803_T_C AX.93252803_T_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93250577_C_C AX.93250577_C_HET AX.93250579_A_C AX.93250579_A_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 1 1 1 1
## 5 0 0 1 1
## 6 1 1 0 0
## AX.93250581_G_C AX.93250581_G_HET AX.93250583_A_C AX.93250583_A_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 2 0 0 0
## 6 0 0 0 0
## AX.93250585_A_C AX.93250585_A_HET AX.93250586_C_C AX.93250586_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 1 1
## AX.93250587_C_C AX.93250587_C_HET AX.93250589_T_C AX.93250589_T_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 2 0 0 0
## AX.93250590_G_C AX.93250590_G_HET AX.93250591_T_A AX.93250591_T_HET
## 1 2 0 0 0
## 2 2 0 NA NA
## 3 NA NA 0 0
## 4 2 0 2 0
## 5 1 1 1 1
## 6 2 0 0 0
## AX.93235772_T_C AX.93235772_T_HET AX.93235773_A_C AX.93235773_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93235774_G_C AX.93235774_G_HET AX.93235777_A_C AX.93235777_A_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 0 0
## 6 0 0 2 0
## AX.93235779_A_C AX.93235779_A_HET AX.93235781_A_C AX.93235781_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93235786_A_C AX.93235786_A_HET AX.93235787_T_C AX.93235787_T_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93235791_G_C AX.93235791_G_HET AX.93235796_A_C AX.93235796_A_HET
## 1 0 0 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 1 1 2 0
## 5 1 1 1 1
## 6 0 0 0 0
## AX.93235799_C_C AX.93235799_C_HET AX.93235805_C_C AX.93235805_C_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93235809_T_C AX.93235809_T_HET AX.93235813_C_C AX.93235813_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93235816_A_C AX.93235816_A_HET AX.93235828_G_C AX.93235828_G_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 1 1
## AX.93235830_A_C AX.93235830_A_HET AX.93235834_G_C AX.93235834_G_HET
## 1 1 1 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 2 0
## 6 2 0 2 0
## AX.93235836_A_C AX.93235836_A_HET AX.93235838_A_C AX.93235838_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93235840_A_C AX.93235840_A_HET AX.93235844_G_C AX.93235844_G_HET
## 1 1 1 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 2 0 0 0
## 5 1 1 0 0
## 6 0 0 2 0
## AX.93235847_C_C AX.93235847_C_HET AX.93235848_A_C AX.93235848_A_HET
## 1 1 1 1 1
## 2 2 0 1 1
## 3 2 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 2 0 0 0
## AX.93239165_A_C AX.93239165_A_HET AX.93239166_T_C AX.93239166_T_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 2 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93239167_T_C AX.93239167_T_HET AX.93239168_C_C AX.93239168_C_HET
## 1 0 0 2 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 2 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93263676_C_C AX.93263676_C_HET AX.93239169_C_C AX.93239169_C_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 2 0 0 0
## AX.93239170_A_C AX.93239170_A_HET AX.93239171_A_C AX.93239171_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93239172_A_C AX.93239172_A_HET AX.93239173_A_C AX.93239173_A_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93239176_C_0 AX.93239176_C_HET AX.93242648_A_C AX.93242648_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 1 1
## 6 0 0 0 0
## AX.93242647_T_C AX.93242647_T_HET AX.93242646_T_C AX.93242646_T_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 0 0
## 5 1 1 1 1
## 6 1 1 2 0
## AX.93242645_G_C AX.93242645_G_HET AX.93242644_G_C AX.93242644_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93242643_T_C AX.93242643_T_HET AX.93242642_G_C AX.93242642_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93262571_A_C AX.93262571_A_HET AX.93234275_C_C AX.93234275_C_HET
## 1 1 1 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 1 1 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93246815_G_A AX.93246815_G_HET AX.93246816_T_C AX.93246816_T_HET
## 1 1 1 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 2 0 1 1
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93246818_C_0 AX.93246818_C_HET AX.93246819_A_C AX.93246819_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93253015_T_C AX.93253015_T_HET AX.93253014_A_C AX.93253014_A_HET
## 1 1 1 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 1 1
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93253007_G_C AX.93253007_G_HET AX.93253005_C_C AX.93253005_C_HET
## 1 1 1 1 1
## 2 0 0 2 0
## 3 0 0 2 0
## 4 0 0 0 0
## 5 1 1 1 1
## 6 0 0 1 1
## AX.93253004_T_C AX.93253004_T_HET AX.93262103_C_C AX.93262103_C_HET
## 1 1 1 0 0
## 2 2 0 0 0
## 3 2 0 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93249246_A_C AX.93249246_A_HET AX.93249245_T_C AX.93249245_T_HET
## 1 2 0 0 0
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 0 0
## 5 1 1 1 1
## 6 1 1 2 0
## AX.93249243_A_C AX.93249243_A_HET AX.93249256_A_C AX.93249256_A_HET
## 1 0 0 1 1
## 2 0 0 2 0
## 3 0 0 2 0
## 4 0 0 0 0
## 5 0 0 2 0
## 6 0 0 1 1
## AX.93249254_T_C AX.93249254_T_HET AX.93249253_C_C AX.93249253_C_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93249251_G_C AX.93249251_G_HET AX.93249250_T_C AX.93249250_T_HET
## 1 1 1 0 0
## 2 2 0 0 0
## 3 2 0 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93249248_C_C AX.93249248_C_HET AX.93235573_C_C AX.93235573_C_HET
## 1 2 0 1 1
## 2 NA NA 0 0
## 3 NA NA 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93235577_T_C AX.93235577_T_HET AX.93235578_G_C AX.93235578_G_HET
## 1 0 0 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 1 1
## 5 1 1 1 1
## 6 1 1 1 1
## AX.93235572_C_C AX.93235572_C_HET AX.93235570_A_C AX.93235570_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93235567_C_C AX.93235567_C_HET AX.93235566_G_C AX.93235566_G_HET
## 1 0 0 2 0
## 2 1 1 1 1
## 3 1 1 1 1
## 4 1 1 0 0
## 5 0 0 0 0
## 6 0 0 2 0
## AX.93235565_C_C AX.93235565_C_HET AX.93235564_T_C AX.93235564_T_HET
## 1 2 0 1 1
## 2 NA NA 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 2 0 0 0
## AX.93235563_T_C AX.93235563_T_HET AX.93235562_G_C AX.93235562_G_HET
## 1 1 1 2 0
## 2 2 0 0 0
## 3 2 0 0 0
## 4 1 1 0 0
## 5 2 0 2 0
## 6 0 0 2 0
## AX.93235560_T_C AX.93235560_T_HET AX.93235559_C_C AX.93235559_C_HET
## 1 0 0 1 1
## 2 0 0 0 0
## 3 0 0 0 0
## 4 1 1 1 1
## 5 0 0 1 1
## 6 0 0 2 0
## AX.93263426_A_C AX.93263426_A_HET AX.93263424_A_C AX.93263424_A_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 1 1 1 1
## 5 1 1 1 1
## 6 0 0 2 0
## AX.93235555_C_C AX.93235555_C_HET AX.93235553_A_C AX.93235553_A_HET
## 1 0 0 0 0
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 1 1
## AX.93235551_C_C AX.93235551_C_HET AX.93235547_A_C AX.93235547_A_HET
## 1 0 0 0 0
## 2 1 1 1 1
## 3 1 1 1 1
## 4 0 0 1 1
## 5 0 0 0 0
## 6 1 1 1 1
## AX.93235546_G_C AX.93235546_G_HET AX.93235545_A_C AX.93235545_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 1 1 0 0
## AX.93235544_G_C AX.93235544_G_HET AX.93235541_T_C AX.93235541_T_HET
## 1 0 0 2 0
## 2 0 0 2 0
## 3 0 0 NA NA
## 4 1 1 1 1
## 5 2 0 1 1
## 6 0 0 1 1
## AX.93235538_G_C AX.93235538_G_HET AX.93235536_G_A AX.93235536_G_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 1 1
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93235535_A_C AX.93235535_A_HET AX.93235533_A_C AX.93235533_A_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 0 0 1 1
## 6 0 0 2 0
## AX.93235532_T_C AX.93235532_T_HET AX.93235530_C_C AX.93235530_C_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 1 1 0 0
## 5 1 1 0 0
## 6 2 0 0 0
## AX.93235529_A_A AX.93235529_A_HET AX.93235526_C_C AX.93235526_C_HET
## 1 1 1 0 0
## 2 2 0 2 0
## 3 2 0 2 0
## 4 1 1 0 0
## 5 1 1 1 1
## 6 0 0 0 0
## AX.93235525_C_C AX.93235525_C_HET AX.93235524_A_C AX.93235524_A_HET
## 1 0 0 0 0
## 2 2 0 1 1
## 3 2 0 1 1
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93235522_T_C AX.93235522_T_HET AX.93235521_C_C AX.93235521_C_HET
## 1 0 0 0 0
## 2 1 1 0 0
## 3 1 1 0 0
## 4 0 0 0 0
## 5 1 1 0 0
## 6 0 0 0 0
## AX.93235520_G_C AX.93235520_G_HET AX.93235518_C_C AX.93235518_C_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 0 0
## 5 0 0 0 0
## 6 0 0 0 0
## AX.93235510_G_C AX.93235510_G_HET AX.93235508_G_C AX.93235508_G_HET
## 1 1 1 1 1
## 2 0 0 2 0
## 3 0 0 2 0
## 4 1 1 0 0
## 5 0 0 1 1
## 6 0 0 2 0
## AX.93235507_G_C AX.93235507_G_HET AX.93235505_G_C AX.93235505_G_HET
## 1 0 0 0 0
## 2 0 0 0 0
## 3 0 0 0 0
## 4 0 0 1 1
## 5 1 1 2 0
## 6 NA NA 1 1
## AX.93235504_T_C AX.93235504_T_HET AX.93235503_A_C AX.93235503_A_HET
## 1 1 1 1 1
## 2 1 1 1 1
## 3 1 1 1 1
## 4 1 1 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93235502_A_C AX.93235502_A_HET AX.93235497_C_C AX.93235497_C_HET
## 1 0 0 1 1
## 2 0 0 1 1
## 3 0 0 1 1
## 4 0 0 0 0
## 5 1 1 0 0
## 6 1 1 0 0
## AX.93259033_G_C AX.93259033_G_HET
## 1 1 1
## 2 1 1
## 3 1 1
## 4 1 1
## 5 0 0
## 6 0 0map_data <- read.table("D.map", header=TRUE, stringsAsFactors=FALSE)
head(map_data)## X0 AX.93233744_C X0.1 X0.2
## 1 0 AX-93233745_T 0 0
## 2 0 AX-93233746_A 0 0
## 3 0 AX-93233747_C 0 0
## 4 0 AX-93233749_G 0 0
## 5 0 AX-93233752_G 0 0
## 6 0 AX-93233753_T 0 0coord <- read.table("D_koordinate.txt", header = TRUE)
head(coord)## id lat lon
## 1 1_3 28.38351 -80.86100
## 2 2_3 28.45910 -80.79395
## 3 3_2 28.48986 -80.69970
## 4 5_1 28.52193 -80.67518
## 5 8_1 28.58668 -80.63023
## 6 9_1 28.66899 -80.60316We can create genind object in order to check for number of individuals, populations and loci.
D_genind <- read.PLINK("D.raw", type = "genind")##
## Reading PLINK raw format into a genlight object...
##
##
## Reading loci information...
##
## Reading and converting genotypes...
## .
## Building final object...
##
## ...done.Number of individuals.
nInd(D_genind)## [1] 72Number of populations:
length(levels(pop(D_genind)))## [1] 6Number of populations can be also represented like this:
nlevels(pop(D_genind))## [1] 6Population names:
pop(D_genind)## [1] Mel Mel Mel Mel Mel Mel Mel Mel Mel Mel Mel Mel PBC PBC PBC
## [16] PBC PBC PBC PBC PBC PBC PBC PBC PBC FM FM FM FM FM FM
## [31] FM FM FM FM FM FM KW16 KW16 KW16 KW16 KW16 KW16 KW16 KW16 KW16
## [46] KW16 KW16 KW16 GG GG GG GG GG GG GG GG GG GG GG GG
## [61] MV MV MV MV MV MV MV MV MV MV MV MV
## Levels: FM GG KW16 Mel MV PBCNumber of individuals in each population:
table(pop(D_genind))##
## FM GG KW16 Mel MV PBC
## 12 12 12 12 12 12Number of loci:
nLoc(D_genind)## [1] 2000Number of loci can be also represented like this:
length(locNames(D_genind))## [1] 2000validObject(D_genind)## [1] TRUESince Adegenet package doesn’t work the best with SNPs it is better if we use DartR for further evaluations. We are using DartR package with genlight objects.
Loading the data
data <- read.PLINK(file="D.raw", map.file = "D.map")This command transform plink files into a genlight object. Genlight object have data about SNPs.
Here we can see number of SNPs, individuals, genotypes and so on:
data## /// GENLIGHT OBJECT /////////
##
## // 72 genotypes, 2,000 binary SNPs, size: 325.3 Kb
## 690 (0.48 %) missing data
##
## // Basic content
## @gen: list of 72 SNPbin
## @ploidy: ploidy of each individual (range: 2-2)
##
## // Optional content
## @ind.names: 72 individual labels
## @loc.names: 2000 locus labels
## @chromosome: factor storing chromosomes of the SNPs
## @position: integer storing positions of the SNPs
## @pop: population of each individual (group size range: 12-12)
## @other: a list containing: sex phenotype pat matWe can get information about populations, names and number.
data@pop## [1] Mel Mel Mel Mel Mel Mel Mel Mel Mel Mel Mel Mel PBC PBC PBC
## [16] PBC PBC PBC PBC PBC PBC PBC PBC PBC FM FM FM FM FM FM
## [31] FM FM FM FM FM FM KW16 KW16 KW16 KW16 KW16 KW16 KW16 KW16 KW16
## [46] KW16 KW16 KW16 GG GG GG GG GG GG GG GG GG GG GG GG
## [61] MV MV MV MV MV MV MV MV MV MV MV MV
## Levels: FM GG KW16 Mel MV PBC# DartR
nPop(data)## [1] 6# also number, base R
nlevels(data@pop)## [1] 6The command we use for getting only the names of the populations is:
unique(data@pop)## [1] Mel PBC FM KW16 GG MV
## Levels: FM GG KW16 Mel MV PBC# or
unique(pop(data))## [1] Mel PBC FM KW16 GG MV
## Levels: FM GG KW16 Mel MV PBCData about individuals, names(ids) and number of individuals:
data$ind.names## [1] "1_3" "2_3" "3_2" "5_1" "8_1" "9_1" "10_2" "11_2" "12_2" "13_2"
## [11] "14_2" "15_2" "3_3" "90" "99" "108" "124" "128" "138" "144"
## [21] "185" "190" "200" "284" "1_4" "2_5" "3_4" "4_1" "5_2" "6_1"
## [31] "8_2" "9_2" "10_3" "11_3" "13_3" "29" "1_5" "2_6" "3_5" "4_2"
## [41] "6_2" "7_2" "18" "20_1" "21_1" "23_1" "24_1" "26_1" "3_9" "5_5"
## [51] "6_6" "7_4" "10_5" "11_5" "12_4" "13_5" "14_4" "15_3" "18_1" "19_1"
## [61] "1_9" "2_10" "3_10" "5_6" "6_7" "7_5" "31_1" "32_1" "33" "34"
## [71] "37" "38"nInd(data)## [1] 72Number of loci:
nLoc(data)## [1] 2000We now need to check if our dataset is valid, this is the command:
data <- gl.compliance.check(data)## Starting gl.compliance.check
## Processing genlight object with SNP data
## The slot loc.all, which stores allele name for each locus, is empty.
## Creating a dummy variable (A/C) to insert in this slot.
## Checking coding of SNPs
## SNP data scored NA, 0, 1 or 2 confirmed
## Checking locus metrics and flags
## Recalculating locus metrics
## Checking for monomorphic loci
## Dataset contains monomorphic loci
## Checking for loci with all missing data
## No loci with all missing data detected
## Checking whether individual names are unique.
## Checking for individual metrics
## Warning: Creating a slot for individual metrics
## Checking for population assignments
## Population assignments confirmed
## Spelling of coordinates checked and changed if necessary to
## lat/lon
## Completed: gl.compliance.checkThere are no errors reported.
3.
Does your data indicate the presence of inbreeding in the population? Give the results of your analysis and interpret the results.
To check for inbreeding in the population we need to check for FIS values (inbreeding coefficient) and the relation between Ho (observed heterozygosity) and He (expected heterozygosity).
If FIS is positive and Ho < He, inbreeding is present. If FIS is close to 0, data us in Hardy-Weinberg equilibrium. If FIS is greater than 0, we have inbreeding. If FIS is smaller than 0, there is no inbreeding.
gl.report.heterozygosity(data)## Starting gl.report.heterozygosity
## Processing genlight object with SNP data
## Calculating Observed Heterozygosities, averaged across
## loci, for each population
## Calculating Expected Heterozygosities
## pop nInd nLoc polyLoc monoLoc all_NALoc Ho HoSD He
## FM 11.923 2000 1637 363 0 0.2662636 0.2156809 0.239767
## GG 11.953 2000 1063 937 0 0.1948894 0.2486188 0.167650
## KW16 11.928 2000 1620 380 0 0.2706000 0.2273341 0.236782
## Mel 11.952 2000 1658 342 0 0.2639000 0.2110112 0.240049
## MV 11.965 2000 1084 916 0 0.1825515 0.2575590 0.146318
## PBC 11.934 2000 1681 319 0 0.2586227 0.2001499 0.243036
## HeSD uHe uHeSD FIS
## 0.166670 0.250262 0.173965 -0.06393986
## 0.185346 0.174969 0.193437 -0.11385336
## 0.169509 0.247141 0.176926 -0.09491973
## 0.163978 0.250529 0.171137 -0.05337015
## 0.178494 0.152699 0.186278 -0.19550086
## 0.162649 0.253664 0.169762 -0.01955022
## Completed: gl.report.heterozygosityWe don’t have positive FIS values, and the observed heterozygosity is higher than the expected, so inbreeding is not present, although the value for PBC is relatively close to 0.
Now let’s check HWE deviation.
The Hardy-Weinberg principle states that in a large, randomly mating population, allele and genotype frequencies will remain constant from generation to generation if other evolutionary influences are not working. These influences include mutation, selection, gene flow, and genetic drift.
Hardy-Weinberg equilibrium allows us to identify loci that may be under selection or experiencing other evolutionary forces.
Ternary plot for each population.
# report for each population separately
gl.report.hwe(data, subset = "each")## Starting gl.report.hwe
## Processing genlight object with SNP data
## Analysing each population separately
## Reporting significant departures from Hardy-Weinberg
## Equilibrium
## NB: Departures significant at the alpha level of 0.05 are listed
## Adjustment of p-values for multiple comparisons vary
## with sample size
## Population Locus Hom_1 Het Hom_2 N Prob Sig
## <char> <char> <int> <int> <int> <num> <num> <char>
## PBC AX-93216306_G_C 9 1 2 12 0.03105590 sig
## PBC AX-93216317_C_C 11 0 1 12 0.04347826 sig
## Mel AX-93216326_A_C 9 1 2 12 0.03105590 sig
## FM AX-93216336_C_C 1 10 0 11 0.01813357 sig
## FM AX-93216336_C_HET 1 10 0 11 0.01813357 sig
## --- --- --- --- --- --- --- ---
## Mel AX-93262226_A_C 10 0 1 11 0.04761905 sig
## PBC AX-93262226_A_C 11 0 1 12 0.04347826 sig
## GG AX-93262571_A_C 7 2 3 12 0.04374748 sig
## KW16 AX-93262571_A_C 9 1 2 12 0.03105590 sig
## KW16 AX-93263625_T_C 2 1 9 12 0.03105590 sig
## Prob.adj Sig.adj npop
## <lgcl> <lgcl> <int>
## NA NA 1
## NA NA 1
## NA NA 1
## NA NA 1
## NA NA 1
## --- --- ---
## NA NA 2
## NA NA 2
## NA NA 2
## NA NA 2
## NA NA 1
##
## Completed: gl.report.hweIn these plots we can see that we have some disequilibrium of homozygotes, but also we have disequilibrium of heterozygotes present. Also what we can observe is that BB allele is nearly absent in 4 out of 6 populations.
Ternary plot for whole dataset.
gl.report.hwe(data, subset = "all")## Starting gl.report.hwe
## Processing genlight object with SNP data
## Pooling all populations for HWE calculations
## Reporting significant departures from Hardy-Weinberg
## Equilibrium
## NB: Departures significant at the alpha level of 0.05 are listed
## Adjustment of p-values for multiple comparisons vary
## with sample size
## Population Locus Hom_1 Het Hom_2 N Prob Sig
## <char> <char> <int> <int> <int> <num> <num> <char>
## pop AX-93216308_T_C 53 14 5 72 1.934411e-02 sig
## pop AX-93216310_T_C 45 19 8 72 2.220949e-02 sig
## pop AX-93216311_G_C 48 17 7 72 1.425047e-02 sig
## pop AX-93216317_C_C 63 5 2 70 1.887787e-02 sig
## pop AX-93216322_C_C 45 16 9 70 2.482724e-03 sig
## --- --- --- --- --- --- --- ---
## pop AX-93262070_T_HET 42 30 0 72 3.031231e-02 sig
## pop AX-93262071_G_HET 42 30 0 72 3.031231e-02 sig
## pop AX-93262226_A_C 59 2 8 69 3.792823e-09 sig
## pop AX-93262571_A_C 35 24 13 72 3.536263e-02 sig
## pop AX-93263224_A_C 42 14 15 71 8.647280e-06 sig
## Prob.adj Sig.adj npop
## <lgcl> <lgcl> <int>
## NA NA 1
## NA NA 1
## NA NA 1
## NA NA 1
## NA NA 1
## --- --- ---
## NA NA 1
## NA NA 1
## NA NA 1
## NA NA 1
## NA NA 1
##
## Completed: gl.report.hweFor the whole dataset, we can observe deviation from Hardy-Weinberg equilibrium, homozygotes AA are not in equilibrium. Additionaly, BB allele is absent. Also, heterozygotes are not in equilibrium. Since FIS values are not positive, this suggests that the observed deviations are not due to inbreeding, but are likely driven by another evolutionary force like genetic drift, selection pressure, or maybe recent migration. Since it seems like allele AA is heading toward fixation and the absence of BB allele is not a matter of sample size, it might be the case that we are dealing with genetic drift.
4.
Calculate the FST between populations and explain genetic differentiation. If present, give possible causes. 2P
FST (Fixation index) is a measure of genetic differentiation between populations. Genetic differentiation is genetic divergence between populations of the same species caused by evolutionary forces.
If we use the argument “nboots,” the program performs 100 bootstrap repetitions to calculate p-values.
fst <- gl.fst.pop(data, nboots=100)
fst$FstsThe highest genetic differentiation is between GG and MV populations.
fst_df <- melt(as.matrix(fst$Fsts))
colnames(fst_df) <- c("Population1", "Population2", "FST")
head(fst_df)## Population1 Population2 FST
## 1 Mel Mel NA
## 2 PBC Mel 0.01292482
## 3 FM Mel 0.02280287
## 4 KW16 Mel 0.03755873
## 5 GG Mel 0.15355031
## 6 MV Mel 0.19810333Plot heatmap:
# Plot heatmap using ggplot2
ggplot(fst_df, aes(x = Population2, y = Population1, fill = FST)) +
geom_tile() +
scale_fill_gradient(low = "white", high = "red", name = "FST") +
theme_minimal() +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
labs(title = "Pairwise FST Heatmap", x = "Population 1", y = "Population 2")
There is high differentiation between MV and other populations and GG
and other populations.
Possible causes for genetic differentiation can be geographic distance. Populations that are geographically closer can have lower FST values since there is higher gene flow because of migration. Another possible cause can be genetic drift, which causes fluctuations of allele frequencies in small populations. Natural selection can be a cause, in which case populations undergo different environmental conditions, so it favors different alleles. Reproductive isolation is also a possible cause.
5.
Calculate the effective size of the populations. On what basis does the command calculate the effective population size? Explain what it is. Which population has the highest and which the lowest estimated effective size? Give the values. 2P
Effective population size
ne <- gl.LDNe(data)## Starting gl.LDNe
## Processing genlight object with SNP data
## Starting gl2genepop
## Processing genlight object with SNP data
## The genepop file is saved as: C:\Users\aleks\AppData\Local\Temp\RtmpCIcNu3/dummy.gen/
## Completed: gl2genepop
## $FM_1
## Statistic Frequency 1 Frequency 2
## Lowest Allele Frequency Used 0+ No S*
## Harmonic Mean Sample Size 11.8 11.8
## Independent Comparisons 1337084 974315
## OverAll r^2 0.140485 0.144573
## Expected r^2 Sample 0.113025 0.108832
## Estimated Ne^ 8.6 6.5
## CI low Parametric 9 6.2
## CI high Parametric 9.3 6.4
## CI low JackKnife 1.9 1.4
## CI high JackKnife Inf Inf
##
## $GG_3
## Statistic Frequency 1 Frequency 2
## Lowest Allele Frequency Used 0+ No S*
## Harmonic Mean Sample Size 11.9 11.9
## Independent Comparisons 563466 444916
## OverAll r^2 0.187406 0.19991
## Expected r^2 Sample 0.110596 0.109016
## Estimated Ne^ 2 1.7
## CI low Parametric 2 1.7
## CI high Parametric 2 1.7
## CI low JackKnife 1 0.8
## CI high JackKnife 9 6.2
##
## $KW16_1
## Statistic Frequency 1 Frequency 2
## Lowest Allele Frequency Used 0+ No S*
## Harmonic Mean Sample Size 11.8 11.8
## Independent Comparisons 1307685 934220
## OverAll r^2 0.131748 0.138135
## Expected r^2 Sample 0.108563 0.110154
## Estimated Ne^ 11.5 8.7
## CI low Parametric 11.1 8.8
## CI high Parametric 11.5 9.1
## CI low JackKnife 3.1 2.5
## CI high JackKnife 102 97.1
##
## $Mel_1
## Statistic Frequency 1 Frequency 2
## Lowest Allele Frequency Used 0+ No S*
## Harmonic Mean Sample Size 11.9 11.9
## Independent Comparisons 1371746 1013166
## OverAll r^2 0.118714 0.120467
## Expected r^2 Sample 0.110881 0.108453
## Estimated Ne^ 34.1 25.6
## CI low Parametric 36.2 23.1
## CI high Parametric 39 24.6
## CI low JackKnife 12.4 8.6
## CI high JackKnife Inf Inf
##
## $MV_1
## Statistic Frequency 1 Frequency 2
## Lowest Allele Frequency Used 0+ No S*
## Harmonic Mean Sample Size 11.9 11.9
## Independent Comparisons 585995 295508
## OverAll r^2 0.221839 0.209289
## Expected r^2 Sample 0.108956 0.110215
## Estimated Ne^ 1.4 1.6
## CI low Parametric 1.4 1.5
## CI high Parametric 1.4 1.6
## CI low JackKnife 0.7 1.1
## CI high JackKnife 2.9 2.4
##
## $PBC_3
## Statistic Frequency 1 Frequency 2
## Lowest Allele Frequency Used 0+ No S*
## Harmonic Mean Sample Size 11.8 11.9
## Independent Comparisons 1409665 1030837
## OverAll r^2 0.109234 0.110855
## Expected r^2 Sample 0.108669 0.110283
## Estimated Ne^ 1875.5 308.7
## CI low Parametric 373.7 350.2
## CI high Parametric 990.9 1139.7
## CI low JackKnife 198.3 134.5
## CI high JackKnife Inf Inf
##
## The results are saved in: C:\Users\aleks\AppData\Local\Temp\RtmpCIcNu3/genepopLD.txt
## Completed: gl.LDNene## $FM_1
## Statistic Frequency 1 Frequency 2
## 1 Lowest Allele Frequency Used 0+ No S*
## 2 Harmonic Mean Sample Size 11.8 11.8
## 3 Independent Comparisons 1337084 974315
## 4 OverAll r^2 0.140485 0.144573
## 5 Expected r^2 Sample 0.113025 0.108832
## 6 Estimated Ne^ 8.6 6.5
## 7 CI low Parametric 9 6.2
## 8 CI high Parametric 9.3 6.4
## 9 CI low JackKnife 1.9 1.4
## 10 CI high JackKnife Inf Inf
##
## $GG_3
## Statistic Frequency 1 Frequency 2
## 1 Lowest Allele Frequency Used 0+ No S*
## 2 Harmonic Mean Sample Size 11.9 11.9
## 3 Independent Comparisons 563466 444916
## 4 OverAll r^2 0.187406 0.19991
## 5 Expected r^2 Sample 0.110596 0.109016
## 6 Estimated Ne^ 2 1.7
## 7 CI low Parametric 2 1.7
## 8 CI high Parametric 2 1.7
## 9 CI low JackKnife 1 0.8
## 10 CI high JackKnife 9 6.2
##
## $KW16_1
## Statistic Frequency 1 Frequency 2
## 1 Lowest Allele Frequency Used 0+ No S*
## 2 Harmonic Mean Sample Size 11.8 11.8
## 3 Independent Comparisons 1307685 934220
## 4 OverAll r^2 0.131748 0.138135
## 5 Expected r^2 Sample 0.108563 0.110154
## 6 Estimated Ne^ 11.5 8.7
## 7 CI low Parametric 11.1 8.8
## 8 CI high Parametric 11.5 9.1
## 9 CI low JackKnife 3.1 2.5
## 10 CI high JackKnife 102 97.1
##
## $Mel_1
## Statistic Frequency 1 Frequency 2
## 1 Lowest Allele Frequency Used 0+ No S*
## 2 Harmonic Mean Sample Size 11.9 11.9
## 3 Independent Comparisons 1371746 1013166
## 4 OverAll r^2 0.118714 0.120467
## 5 Expected r^2 Sample 0.110881 0.108453
## 6 Estimated Ne^ 34.1 25.6
## 7 CI low Parametric 36.2 23.1
## 8 CI high Parametric 39 24.6
## 9 CI low JackKnife 12.4 8.6
## 10 CI high JackKnife Inf Inf
##
## $MV_1
## Statistic Frequency 1 Frequency 2
## 1 Lowest Allele Frequency Used 0+ No S*
## 2 Harmonic Mean Sample Size 11.9 11.9
## 3 Independent Comparisons 585995 295508
## 4 OverAll r^2 0.221839 0.209289
## 5 Expected r^2 Sample 0.108956 0.110215
## 6 Estimated Ne^ 1.4 1.6
## 7 CI low Parametric 1.4 1.5
## 8 CI high Parametric 1.4 1.6
## 9 CI low JackKnife 0.7 1.1
## 10 CI high JackKnife 2.9 2.4
##
## $PBC_3
## Statistic Frequency 1 Frequency 2
## 1 Lowest Allele Frequency Used 0+ No S*
## 2 Harmonic Mean Sample Size 11.8 11.9
## 3 Independent Comparisons 1409665 1030837
## 4 OverAll r^2 0.109234 0.110855
## 5 Expected r^2 Sample 0.108669 0.110283
## 6 Estimated Ne^ 1875.5 308.7
## 7 CI low Parametric 373.7 350.2
## 8 CI high Parametric 990.9 1139.7
## 9 CI low JackKnife 198.3 134.5
## 10 CI high JackKnife Inf InfThe effective population size is estimated using the gl.LDNe() function. The function estimates Ne based on linkage disequilibrium (LD). Linkage disequilibrium happens when two loci are close to each other and are inherited together since they don’t undergo separation in recombination during meiosis.
In small populations LD tends to be higher because of presence of genetic drift.
Population that has the highest effective population size is PBC with value above 1750, and the ones with the lowest are GG and MV, around 0. The others are pretty close to 0 too.
6.
Calculate and then produce a PCA plot. Explain what the plot represents (interpret the results of the analysis). What can you tell about the structure of your dataset?
Calculate principle components:
pca <- gl.pcoa(data)## Starting gl.pcoa
## Processing genlight object with SNP data
## Performing a PCA, individuals as entities, loci as attributes, SNP genotype as state
## Completed: gl.pcoaScree Plot explains the PCA and decides how many components need to be preserved. The first principal component (value 1 on the PCA Axis) contributes to the explanation of about 12% of the variance in our data, the second explains 9%. After PC2, the variance contribution drops sharply to PC3, which means the first three principal components capture the most genetic variation.
gl.pcoa.plot(x = data, glPca = pca)## Starting gl.pcoa.plot
## Processing an ordination file (glPca)
## Processing genlight object with SNP data
## Plotting populations in a space defined by the SNPs
## Preparing plot .... please wait
## Completed: gl.pcoa.plotOn the X-axis we have the 1st component, which explains 11.7% of the variance and on the Y-axis the 2nd component, which explains 8.8% of the variance. From the graph, we can see that the MV population differs the most from the other 5 populations.Also GG differs but not that much. The other 4 populations do not differ from each other,they are clustered together.
gl.pcoa.plot(x = data, glPca = pca, zaxis = 3)## Starting gl.pcoa.plot
## Processing an ordination file (glPca)
## Processing genlight object with SNP data
## Displaying a three dimensional plot, mouse over for details for each point
## May need to zoom out to place 3D plot within bounds
## Completed: gl.pcoa.plotFrom the 3D representation we can see that MV and GG form more separate clusters than the others as in the 2D plot, with the difference that now we can see that KW16 is also being somewhat to the side and forming a separate cluster, which we couldn’t see from the 2D representation.That’s why it is good to use a 3D plot.
GG and MV are forming their own distinct clusters, and FM and KW16 are showing more admixture, forming a gradient instead of strict clusters. Mel and PBC are overlapping with FM and KW16, so probably they share ancestry or gene flow with them. MV and GG forms their own clusters, which connects us to the highest genetic differentiation between these two populations and the other populations.
NEIGHBOUR JOINING TREE
gl.tree.nj(data, type = "phylogram")## Starting gl.tree.nj
## Processing genlight object with SNP data
## Converting to a matrix of frequencies, locus by populations
## Computing Euclidean distances
## Completed: gl.tree.nj##
## Phylogenetic tree with 6 tips and 4 internal nodes.
##
## Tip labels:
## FM, GG, KW16, Mel, MV, PBC
##
## Unrooted; includes branch length(s).MV and GG populations have long branches, which means they have high genetic differentiation and no recent gene flow with other populations.
KW16 and FM share a more recent common ancestor compared to most of the other populations, but a more distant one than Mel and PBC.
The branch connecting Mel and PBC is short, which means that there has been relatively little evolutionary change (genetic drift, mutation) differentiating them since they shared a common ancestor.
So, on both the dendrogram and the PCA plot Mel and PBC as the most similar pair.
Both methods also overlap on the close relationship between KW16 and FM, although they are not as tightly clustered as Mel and PBC in the PCA.
Both the dendrogram and PCA represent the genetic distinction of GG and MV from the other populations.
STRUCTURE
The STRUCTURE program allows the analysis of different populations, assigning individuals to populations, studying hybrid zones, identifying migrants and mixed individuals.
str <- gl.run.structure(data, k.range= 1:6, num.k.rep = 2, exec = "structure.exe", numreps=200, burnin=100)## Starting gl.run.structure
## Processing genlight object with SNP data
## Completed: gl.run.structureFor us, the \(\Delta\)K graph is important. The command gl.evanno(str) \(\Delta\)K estimates the number of calculated subpopulations that best estimate the structure of our data. We look at \(\Delta\)K with the highest value. In this case, the highest value is 5.
gl.evanno(str)
## $df
## k reps mean.ln.k sd.ln.k ln.pk ln.ppk delta.k
## 1 1 2 -113241.8 29.769195 NA NA NA
## 2 2 2 -108983.5 886.146218 4258.25 55.25 0.06234863
## 3 3 2 -104780.5 9.899495 4203.00 5817.30 587.63603974
## 4 4 2 -106394.8 1865.771953 -1614.30 2953.15 1.58280330
## 5 5 2 -105055.9 44.194174 1338.85 1295.05 29.30363638
## 6 6 2 -105012.1 152.805775 43.80 NA NA
##
## $plots
## $plots$mean.ln.k
##
## $plots$ln.pk
##
## $plots$ln.ppk
##
## $plots$delta.k
This graph is showing the ΔK values, which are used to determine the most likely number of distinct genetic clusters/populations.
A sharp peak at K=5 means that 5 is the most likely number of clusters, so the individuals in the dataset can be divided into five groups that are genetically different from each other.
To draw a graph of population structure we use the command:
gl.evanno(str)
## $df
## k reps mean.ln.k sd.ln.k ln.pk ln.ppk delta.k
## 1 1 2 -113241.8 29.769195 NA NA NA
## 2 2 2 -108983.5 886.146218 4258.25 55.25 0.06234863
## 3 3 2 -104780.5 9.899495 4203.00 5817.30 587.63603974
## 4 4 2 -106394.8 1865.771953 -1614.30 2953.15 1.58280330
## 5 5 2 -105055.9 44.194174 1338.85 1295.05 29.30363638
## 6 6 2 -105012.1 152.805775 43.80 NA NA
##
## $plots
## $plots$mean.ln.k
##
## $plots$ln.pk
##
## $plots$ln.ppk
##
## $plots$delta.k
gl.plot.structure(str, K=2)## Starting gl.plot.structure
## Completed: gl.plot.structuregl.plot.structure(str, K=3)## Starting gl.plot.structure
## Completed: gl.plot.structuregl.plot.structure(str, K=4)## Starting gl.plot.structure
## Completed: gl.plot.structuregl.plot.structure(str, K=5)## Starting gl.plot.structure
## Completed: gl.plot.structureMV is represented as distinct population at K=5, which is confirmed by the PCA and the FST values. GG is distinct for all K values, showing no admixture, supported by PCA and FST. The populations FM and KW16 show continuous variation, which indicates common ancestry or historical admixture. Mel and PBC are mostly red, but show some variability, have recent admixture.
7.
Does the calculated isolation by distance indicate isolation of populations? Please comment.
The correlation of genetic diversity between individuals decreases as a function of geographic distance. Migration is usually localized in space, which is why individuals from nearby subpopulations are expected to be more genetically similar.The IBD command calculates the FST distance and the Euclidean distance (distance in space between individuals).
coordinates <- read.table("D_koordinate.txt",header = T)
as.data.frame(coordinates)## id lat lon
## 1 1_3 28.38351 -80.86100
## 2 2_3 28.45910 -80.79395
## 3 3_2 28.48986 -80.69970
## 4 5_1 28.52193 -80.67518
## 5 8_1 28.58668 -80.63023
## 6 9_1 28.66899 -80.60316
## 7 10_2 28.67131 -80.60089
## 8 11_2 28.68660 -80.59389
## 9 12_2 28.76809 -80.58664
## 10 13_2 28.82765 -80.57171
## 11 14_2 28.84794 -80.47549
## 12 15_2 28.85964 -80.43145
## 13 3_3 26.72200 -80.41735
## 14 90 26.75146 -80.33422
## 15 99 26.77550 -80.30058
## 16 108 26.83108 -80.23237
## 17 124 26.92929 -80.22784
## 18 128 26.96413 -80.13759
## 19 138 27.05090 -80.10414
## 20 144 27.09555 -80.09261
## 21 185 27.13165 -79.99944
## 22 190 27.14187 -79.97806
## 23 200 27.18180 -79.90452
## 24 284 27.23546 -79.87980
## 25 1_4 26.67532 -81.65894
## 26 2_5 26.72812 -81.64386
## 27 3_4 26.78103 -81.58905
## 28 4_1 26.78257 -81.50051
## 29 5_2 26.85402 -81.40285
## 30 6_1 26.85458 -81.34886
## 31 8_2 26.88110 -81.30132
## 32 9_2 26.92853 -81.21521
## 33 10_3 26.96437 -81.20300
## 34 11_3 27.01076 -81.13532
## 35 13_3 27.04317 -81.12838
## 36 29 27.12150 -81.07854
## 37 1_5 25.07614 -81.78424
## 38 2_6 25.11529 -81.73620
## 39 3_5 25.13406 -81.66986
## 40 4_2 25.14318 -81.64972
## 41 6_2 25.15786 -81.62072
## 42 7_2 25.23635 -81.55161
## 43 18 25.26566 -81.48095
## 44 20_1 25.32258 -81.41023
## 45 21_1 25.38406 -81.32932
## 46 23_1 25.40648 -81.26365
## 47 24_1 25.47800 -81.22928
## 48 26_1 25.52140 -81.20662
## 49 3_9 33.67975 -117.51249
## 50 5_5 33.70964 -117.50067
## 51 6_6 33.76716 -117.43522
## 52 7_4 33.82353 -117.41326
## 53 10_5 33.92078 -117.33045
## 54 11_5 33.92621 -117.23190
## 55 12_4 33.93673 -117.15715
## 56 13_5 33.93888 -117.13832
## 57 14_4 33.94749 -117.13420
## 58 15_3 34.00710 -117.07106
## 59 18_1 34.04740 -117.02310
## 60 19_1 34.09604 -116.96714
## 61 1_9 33.60700 -117.50743
## 62 2_10 33.65287 -117.43607
## 63 3_10 33.66657 -117.41446
## 64 5_6 33.68696 -117.31534
## 65 6_7 33.70411 -117.27106
## 66 7_5 33.72575 -117.24889
## 67 31_1 33.81423 -117.22504
## 68 32_1 33.87666 -117.19616
## 69 33 33.90794 -117.12271
## 70 34 33.93775 -117.04865
## 71 37 33.94334 -117.00918
## 72 38 33.98418 -116.96034gl.ibd(data, coordinates = coordinates[,2-3], distance = "Fst")## Analysis performed on the genlight object.## 'nperm' >= set of all permutations: complete enumeration.## Set of permutations < 'minperm'. Generating entire set.
## Coordinates used from: data.frame lat/lon (Mercator transformed)
## Transformation of Dgeo: Dgeo
## Genetic distance: Fst
## Tranformation of Dgen: Dgen
##
## Mantel statistic based on Pearson's product-moment correlation
##
## Call:
## vegan::mantel(xdis = Dgen, ydis = Dgeo, permutations = permutations, na.rm = TRUE)
##
## Mantel statistic r: 0.633
## Significance: 0.041667
##
## Upper quantiles of permutations (null model):
## 90% 95% 97.5% 99%
## 0.234 0.631 0.634 0.634
## Permutation: free
## Number of permutations: 719
##
##
## Completed: gl.ibd## $Dgen
## FM GG KW16 Mel MV
## GG 0.14540894
## KW16 0.04290602 0.17089061
## Mel 0.02280287 0.15355031 0.03755873
## MV 0.19719878 0.28493627 0.21905184 0.19810333
## PBC 0.01961675 0.14332658 0.03340314 0.01292482 0.18688499
##
## $Dgeo
## FM GG KW16 Mel MV
## GG 4097009.18
## KW16 200846.64 4130460.12
## Mel 235888.90 4133149.41 432827.36
## MV 4092392.80 14521.24 4125185.89 4129320.23
## PBC 135975.40 4226547.05 260977.44 216437.83 4222067.05
##
## $mantel
##
## Mantel statistic based on Pearson's product-moment correlation
##
## Call:
## vegan::mantel(xdis = Dgen, ydis = Dgeo, permutations = permutations, na.rm = TRUE)
##
## Mantel statistic r: 0.633
## Significance: 0.041667
##
## Upper quantiles of permutations (null model):
## 90% 95% 97.5% 99%
## 0.234 0.631 0.634 0.634
## Permutation: free
## Number of permutations: 719The x-axis shows the geographical distance, and the y-axis shows the genetic distance. Because the slope of the line is positive (goes up), we can conclude that we have isolation with distance in our dataset. The result is statistically significant because since p < 0.05, but R² = 0.401 which means while distance plays a role, other factors like historical migration, environmental barriers and selection influence genetic structure.
Density plot.
#Prepare the matrices
Dgeo <- as.matrix(dist(coordinates[,2-3]))
Dgen <- as.matrix(dist(as.matrix(data)))
#Calculate density
dens <- kde2d(as.vector(Dgeo), as.vector(Dgen), n=300)
#Create color palette
myPal <- colorRampPalette(c("white", "blue", "gold", "orange", "red"))
#Plot all together
plot(Dgeo, Dgen, pch=20,cex=.5)
image(dens, col=transp(myPal(300),.7), add=TRUE)
# Calculate distance
dist_lm <- lm(as.vector(Dgen) ~ as.vector(Dgeo))
abline(dist_lm)
title("Isolation by distance plot")