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

Table 3 Median genotype concordance between designated SNP callers for overlapping SNP sites assessed at the individual level

	GATK-CLC	SAMtools- GATK	SAMtools-CLC
% same genotype called Pop_WA	96.92	98.46	96.15
% same genotype called Pop_SK	98.27	98.04	97.45
% same genotype called overall	97.51	98.32	97.24
% same genotype called overall (range)	93.59-98.38	97.08-99.26	92.46-97.82

ISSN: 1471-2164