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)
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 |