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Table 5 Concordance between genotype calls with different levels of conservativeness from low- and high-coverage sequence data, 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|0b 1|0 2|0 0|1 1|1 2|1 0|2 1|2 2|2
Best-guess
 1× 30,875 62.6 81.1 99.45 0.55 51.35 48.65 0.70 99.30
 2× 35,688 79.9 90.0 98.60 1.40 0.00 26.20 48.26 25.54 0.04 1.61 98.35
 3× 28,357 88.6 94.3 98.36 1.64 0.00 13.80 72.20 14.00 0.00 2.22 97.78
 4× 17,849 92.7 96.4 98.05 1.95 0.00 8.22 84.01 7.77 0.00 2.63 97.37
 5× 9619 95.3 97.6 97.40 2.60 0.00 4.55 91.52 3.93 0.00 2.49 97.51
 6–10× 7047 95.2 97.6 97.73 2.27 0.00 4.96 91.05 4.00 0.00 2.68 97.32
 Overall 129,435 81.4 90.7 98.53 1.34 0.13 24.27 52.40 23.33 0.18 1.61 98.21
Probability ≥ 0.90
 1× 0
 2–3×b 14,572 95.5 97.7 100.00 100.00 100.00
 4× 14,359 92.7 96.3 99.97 0.03 0.00 16.24 68.39 15.37 0.00 0.05 99.95
 5× 8315 96.3 98.2 99.92 0.08 0.00 6.76 87.41 5.83 0.00 0.10 99.90
 6–10× 6397 98.1 99.0 99.83 0.17 0.00 3.08 94.65 2.27 0.00 0.29 99.71
 Overall 43,643 95.1 97.5 97.18 2.82 0.00 3.52 93.26 3.21 0.00 3.65 96.35
Probability ≥ 0.98
 1–3× 0
 4–5×b 4366 99.8 99.9 100.00 100.00 100.00
 6–10× 6313 98.1 99.1 99.83 0.17 0.00 3.15 94.58 2.26 0.00 0.29 99.71
 Overall 10,679 98.8 99.4 99.65 0.35 0.00 1.00 98.28 0.72 0.00 0.57 99.43
  1. aNumber of genotypes called for 5,531 SNPs across 26 individuals
  2. bHeterozygotes are easier to call than homozygotes; at these coverages, certainty is not sufficient to call the homozygotes, but note, that the actual counts for (1|0) and (1|2) are very low compared to (1|1): 19-fold and 569-fold lower for genotypes called with a probability greater than 0.90 and 0.98, respectively
  3. Concordance is shown by coverage at variant site