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Table 3 Concordance of best-guess genotype calls from sequence data with SNP array genotypes, using allele read counts obtained with the default settings of GATK HaplotypeCaller

From: Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing

  na Genotype concordance (%) Allele concordance (%) Concordance by genotype (%)
True = 0 True = 1 True = 2
0|0 1|0 2|0 0|1 1|1 2|1 0|2 1|2 2|2
Low coverage
 1× 27,185 42.2 61.0 99.97 0.03 95.14 4.86 81.96 18.04
 2× 33,638 57.2 76.0 99.94 0.00 0.06 72.87 3.51 23.62 20.07 0.25 79.68
 3× 24,789 70.3 84.5 99.91 0.08 0.01 56.37 31.87 11.76 6.23 1.45 92.32
 4× 14,015 79.7 89.6 99.85 0.13 0.02 43.11 51.44 5.46 2.14 1.69 96.16
 5× 6502 85.6 92.7 99.93 0.04 0.04 32.65 64.75 2.59 0.90 1.96 97.14
 6–10× 3705 90.5 95.2 99.83 0.12 0.06 22.47 74.68 2.85 0.61 1.07 98.32
 Overall 109,834 62.1 77.6 99.92 0.04 0.03 66.41 21.50 12.09 29.84 0.71 69.45
High coverage 131,806 99.7 99.9 99.80 0.19 0.01 0.21 99.72 0.07 0.17 0.16 99.68
  1. aNumber of genotypes called across 26 individuals at 5136 and 5531 SNPs for low- and high-coverage data, respectively
  2. Concordance is shown by coverage at variant site