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Table 4 Overview of genotype validations at overlapping SNP sites

From: Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms

  SNPs validated Genotypes validated True CLC True GATK/SAMtools
Category    n % n %
Discordant calls a       
Singleton site determined by GATK/SAMtoolsb 8 8 1 12.5 7 87.50
Singleton site determined by CLCb 4 4 0 0.00 4 100
Homozygote with GATK/SAMtools but heterozygote with CLC 23 28 3 10.71 25 89.29
Heterozygote with GATK/SAMtools but homozygote with CLC 23 23 7 30.43 16 69.57
Total 58 63 11 17.46 52 82.54
Concordant calls c       
Total 53 114 110 (96.49%)
  1. aOverlapping SNP sites but discordant genotype assignments. bLoci were exclusively counted in this category without considering them in the homo- or heterozygote categories below. c100 of the 114 genotypes were validated from the same sites used to validate the discordant genotypes. The remaining 14 genotypes were validated from 14 SNPs chosen randomly from the GATK-CLCintersect dataset (exclusively identical genotype calls).