Table 4 Comparison of concordance between BWA-MEM and HLA-LA for development batch
From: A computational HLA allele-typing protocol to de-noise and leverage nanopore amplicon data
Gene | P-Value | BWA-MEM Concordance | HLA-LA Concordance | Difference |
|---|---|---|---|---|
HLA-A | 1.00E + 00 | 98.4% | 98.4% | ns |
HLA-B | 3.71E-01 | 96.8% | 91.9% | ns |
HLA-C | 6.17E-01 | 98.4% | 95.2% | ns |
HLA-DPA1 | 6.17E-01 | 96.8% | 93.5% | ns |
HLA-DPB1 | 4.55E-02 | 98.4% | 87.1% | BWA-MEM higher concordance* |
HLA-DQA1 | 9.44E-07 | 98.4% | 56.5% | BWA-MEM higher concordance* |
HLA-DQB1 | 1.34E-01 | 98.4% | 91.9% | ns |
HLA-DRB1 | 2.20E-03 | 64.5% | 90.3% | HLA-LA higher concordance* |
HLA-DRB3 | 7.36E-02 | 73.9% | 95.7% | ns |
HLA-DRB4 | 8.74E-04 | 100.0% | 18.8% | BWA-MEM higher concordance* |
Overall | 3.54E-04 | 93.1% | 86.4% | BWA-MEM higher concordance* |