Skip to main content

Table 1 Genotype concordance metrics

From: Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

  Genotype concordance Non-reference sensitivity
  GATK Freebayes SAMtools GATK Freebayes SAMtools
  No.SNPs Mean ± SD No.SNPs Mean ± SD No.SNPs Mean ± SD No.SNPs Mean ± SD No.SNPs Mean ± SD No.SNPs Mean ± SD
≤0.1 23 0.03 ± 0.03 9 0.03 ± 0.03 3 0.08 ± 0.00 3 0.01 ± 0.02 9 0.04 ± 0.04 5 0.04 ± 0.04
≤0.2 18 0.14 ± 0.03 6 0.15 ± 0.03 6 0.15 ± 0.02 13 0.15 ± 0.03 10 0.14 ± 0.03 15 0.14 ± 0.03
≤0.3 12 0.25 ± 0.02 9 0.27 ± 0.02 9 0.25 ± 0.03 25 0.25 ± 0.03 7 0.24 ± 0.03 20 0.24 ± 0.03
≤0.4 13 0.33 ± 0.02 5 0.33 ± 0.01 18 0.35 ± 0.03 20 0.34 ± 0.02 11 0.34 ± 0.03 19 0.34 ± 0.03
≤0.5 22 0.45 ± 0.03 18 0.45 ± 0.03 24 0.45 ± 0.03 20 0.45 ± 0.02 14 0.45 ± 0.03 24 0.44 ± 0.03
≤0.6 42 0.55 ± 0.03 39 0.55 ± 0.04 43 0.55 ± 0.03 59 0.52 ± 0.03 89 0.51 ± 0.02 82 0.51 ± 0.03
≤0.7 73 0.65 ± 0.03 64 0.66 ± 0.03 62 0.66 ± 0.03 96 0.66 ± 0.02 105 0.66 ± 0.02 158 0.66 ± 0.03
≤0.8 110 0.76 ± 0.03 183 0.76 ± 0.03 123 0.76 ± 0.03 152 0.75 ± 0.02 150 0.75 ± 0.02 215 0.75 ± 0.02
≤0.9 679 0.87 ± 0.03 3828 0.88 ± 0.02 738 0.87 ± 0.03 1206 0.86 ± 0.03 1171 0.86 ± 0.03 1561 0.86 ± 0.03
≤1 50441 0.98 ± 0.02 46725 0.97 ± 0.02 50334 0.98 ± 0.02 49732 0.99 ± 0.02 49206 0.99 ± 0.02 49148 0.99 ± 0.02
  Non-reference genotype concordance Precision
≤0.1 55 0.02 ± 0.03 34 0.02 ± 0.03 35 0.02 ± 0.03 46 0.02 ± 0.04 28 0.01 ± 0.03 28 0.01 ± 0.03
≤0.2 18 0.13 ± 0.03 10 0.14 ± 0.03 23 0.14 ± 0.03 11 0.14 ± 0.03 12 0.15 ± 0.03 11 0.16 ± 0.03
≤0.3 24 0.26 ± 0.03 20 0.25 ± 0.03 24 0.25 ± 0.03 22 0.25 ± 0.03 22 0.25 ± 0.03 17 0.25 ± 0.03
≤0.4 32 0.34 ± 0.02 35 0.34 ± 0.02 43 0.35 ± 0.02 26 0.35 ± 0.03 21 0.34 ± 0.02 20 0.35 ± 0.03
≤0.5 32 0.43 ± 0.03 41 0.43 ± 0.03 38 0.43 ± 0.03 15 0.42 ± 0.02 36 0.43 ± 0.03 21 0.44 ± 0.03
≤0.6 144 0.52 ± 0.03 249 0.52 ± 0.03 168 0.52 ± 0.03 99 0.52 ± 0.03 161 0.52 ± 0.03 99 0.53 ± 0.03
≤0.7 245 0.66 ± 0.03 540 0.66 ± 0.03 297 0.65 ± 0.03 157 0.66 ± 0.03 499 0.66 ± 0.03 156 0.66 ± 0.03
≤0.8 445 0.75 ± 0.02 1725 0.76 ± 0.03 584 0.76 ± 0.02 270 0.75 ± 0.02 2246 0.76 ± 0.02 240 0.75 ± 0.02
≤0.9 3019 0.86 ± 0.03 6607 0.86 ± 0.03 3720 0.86 ± 0.03 1644 0.86 ± 0.03 6808 0.85 ± 0.03 1964 0.86 ± 0.03
≤1 47312 0.98 ± 0.03 41511 0.97 ± 0.03 46315 0.98 ± 0.03 49038 0.99 ± 0.02 40941 0.97 ± 0.03 48692 0.98 ± 0.03
  1. The calculation based on array genotypes and corresponding sequence-based genotypes obtained with different variant callers at positions where SNPs from the array were available on chromosomes 3, 6 and 28