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