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Table 9 Impact of level of index hopping on concordance between low- and high-coverage sequence data

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

  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
 0% 82.2 91.1 99.63 0.34 0.03 23.65 52.82 23.53 0.04 0.47 99.49
 0.1% 82.4 91.2 99.55 0.41 0.03 23.67 53.36 22.97 0.08 0.49 99.43
 0.5% 82.2 91.1 99.30 0.64 0.06 23.97 53.08 22.96 0.10 0.89 99.01
 1% 81.9 90.9 99.03 0.87 0.10 23.77 53.09 23.14 0.14 1.28 98.58
 2% 81.3 90.6 98.25 1.59 0.16 23.79 52.78 23.43 0.23 2.07 97.70
 5% 80.1 89.9 96.45 3.17 0.37 23.63 53.23 23.14 0.59 4.58 94.82
Probability ≥ 0.90
 0% 96.9 98.5 99.20 0.80 0.00 2.46 94.98 2.55 0.00 1.16 98.84
 0.1% 96.7 98.3 99.01 0.99 0.00 2.59 94.70 2.71 0.00 1.26 98.74
 0.5% 96.4 98.2 98.39 1.61 0.00 2.59 94.75 2.66 0.00 1.98 98.02
 1% 96.2 98.1 97.87 2.13 0.00 2.68 94.99 2.33 0.00 2.98 97.02
 2% 95.4 97.7 96.36 3.64 0.00 2.59 94.85 2.56 0.00 4.92 95.08
 5% 93.2 96.6 92.53 7.47 0.00 2.65 94.78 2.57 0.00 10.55 89.45
Probability ≥ 0.98
 0% 99.4 99.7 100.00 0.00 0.00 0.53 99.03 0.44 0.00 0.00 100.00
 0.1% 99.3 99.6 100.00 0.00 0.00 0.63 98.85 0.53 0.00 0.00 100.00
 0.5% 99.4 99.7 99.95 0.05 0.00 0.37 99.09 0.54 0.00 0.09 99.91
 1% 99.2 99.6 99.82 0.18 0.00 0.51 98.97 0.52 0.00 0.46 99.54
 2% 99.1 99.5 99.47 0.53 0.00 0.52 98.89 0.59 0.00 0.75 99.25
 5% 98.6 99.3 98.42 1.58 0.00 0.59 98.94 0.47 0.00 2.83 97.17