Agreement amongst variant calling programs. Variants were detected jointly on ten samples from The 1000 Genomes Project using FreeBayes, SamTools, GATK, and Atlas, as in Figure 1. A. For each SNP, agreement amongst the variant calling programs was calculated. The number of SNPs detected by each of the programs is indicated by the number in the enclosing ellipses. B. Agreement amongst the variant calling programs displayed as a barplot. A = Atlas, F = FreeBayes, G = GATK, S = Samtools. Left-hand y-axis indicates number of SNPs detected by the programs denoted on the x-axis. Right-hand y-axis indicates the percent of all SNPs detected by the programs denoted on the x-axis.