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× | 27,185 | 42.2 | 61.0 | 99.97 | – | 0.03 | 95.14 | – | 4.86 | 81.96 | – | 18.04 |
2× | 33,638 | 57.2 | 76.0 | 99.94 | 0.00 | 0.06 | 72.87 | 3.51 | 23.62 | 20.07 | 0.25 | 79.68 |
3× | 24,789 | 70.3 | 84.5 | 99.91 | 0.08 | 0.01 | 56.37 | 31.87 | 11.76 | 6.23 | 1.45 | 92.32 |
4× | 14,015 | 79.7 | 89.6 | 99.85 | 0.13 | 0.02 | 43.11 | 51.44 | 5.46 | 2.14 | 1.69 | 96.16 |
5× | 6502 | 85.6 | 92.7 | 99.93 | 0.04 | 0.04 | 32.65 | 64.75 | 2.59 | 0.90 | 1.96 | 97.14 |
6–10× | 3705 | 90.5 | 95.2 | 99.83 | 0.12 | 0.06 | 22.47 | 74.68 | 2.85 | 0.61 | 1.07 | 98.32 |
Overall | 109,834 | 62.1 | 77.6 | 99.92 | 0.04 | 0.03 | 66.41 | 21.50 | 12.09 | 29.84 | 0.71 | 69.45 |
High coverage | 131,806 | 99.7 | 99.9 | 99.80 | 0.19 | 0.01 | 0.21 | 99.72 | 0.07 | 0.17 | 0.16 | 99.68 |