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

Table 4 Overview of genotype validations at overlapping SNP sites

	SNPs validated	Genotypes validated	True CLC		True GATK/SAMtools
Category			n	%	n	%
*Discordant calls* ^a
Singleton site determined by GATK/SAMtools^b	8	8	1	12.5	7	87.50
Singleton site determined by CLC^b	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%)

^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-CLC_intersect dataset (exclusively identical genotype calls).

ISSN: 1471-2164