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Table 4 Concordance of best-guess genotype calls from sequence data with SNP array genotypes, using allele read counts obtained from aligned reads in BAM files

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× 28,300 62.1 80.8 99.34 0.66 51.46 48.54 0.96 99.04
 2× 32,699 79.5 89.7 98.42 1.53 0.05 26.41 48.15 25.44 0.21 1.70 98.09
 3× 25,993 88.3 94.1 98.25 1.72 0.03 14.01 71.98 14.01 0.12 2.36 97.52
 4× 16,346 92.5 96.3 97.91 2.09 0.00 8.36 83.84 7.80 0.00 2.77 97.23
 5× 8878 94.9 97.5 97.28 2.72 0.00 4.83 91.15 4.02 0.16 2.81 97.03
 6–10× 6444 95.0 97.5 97.43 2.50 0.07 5.01 91.09 3.90 0.00 2.75 97.25
 Overall 118,660 81.1 90.5 98.39 1.43 0.18 24.43 52.30 23.27 0.33 1.71 97.96
High coverage 131,782 99.8 99.9 99.80 0.19 0.01 0.12 99.81 0.07 0.10 0.17 99.73
  1. aNumber of genotypes called for 5531 SNPs across 26 individuals both for low- and high-coverage data
  2. Concordance is shown by coverage at variant site