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Table 7 Impact of bias towards the reference allele due to alignment on concordance between low- and high-coverage sequence data by alignment with the original reference genome (REF), the tailored reference genome (ALT), or a combination of both (CIS and TRANS)

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
Best-guess
 REF 129,435 81.4 90.7 98.53 1.34 0.13 24.27 52.40 23.33 0.18 1.61 98.21
 ALT 129,327 81.4 90.7 98.36 1.49 0.14 23.66 52.42 23.92 0.17 1.47 98.36
 CIS 129,610 81.5 90.7 98.37 1.49 0.14 23.82 52.73 23.45 0.17 1.62 98.21
 TRANS 129,148 81.3 90.6 98.52 1.34 0.13 24.11 52.10 23.79 0.18 1.46 98.36
Probability ≥ 0.90
 REF 43,643 95.1 97.5 97.18 2.82 0.00 3.52 93.26 3.21 0.00 3.65 96.35
 ALT 43,489 95.0 97.5 96.75 3.25 0.00 3.35 93.30 3.36 0.00 3.22 96.78
 CIS 43,970 95.0 97.5 96.88 3.12 0.00 3.44 93.30 3.26 0.00 3.52 96.48
 TRANS 43,145 95.1 97.6 97.10 2.90 0.00 3.42 93.28 3.30 0.00 3.32 96.68
Probability ≥ 0.98
 REF 10,679 98.8 99.4 99.65 0.35 0.00 1.00 98.28 0.72 0.00 0.57 99.43
 ALT 10,638 98.8 99.4 99.64 0.36 0.00 0.92 98.26 0.81 0.00 0.41 99.59
 CIS 10,858 98.8 99.4 99.65 0.35 0.00 0.98 98.23 0.78 0.00 0.55 99.45
 TRANS 10,463 98.8 99.4 99.64 0.36 0.00 0.94 98.31 0.75 0.00 0.43 99.57
  1. aNumber of genotypes called for 5531 SNPs across 26 individuals