MHC haplotype accuracy
| Haplotype | Pipeline errors (bp) | Coverage errors (bp) | Sequence complexity errors (bp) | Bionano DLE-1 discrepancies (6 bp) | HLA sequence errors (bp) | Microarray errors (bp) | Total errors (bp) | Assembly accuracy % (identity) |
|---|---|---|---|---|---|---|---|---|
| PGF | 13 | 367 | 185 | NA | NA | NA | 565 | 99.98 |
| COX | 178 | 3763 | 116 | NA | NA | NA | 4057 | 99.89 |
| EAS-P-1 | 78 | 38 | 114 | NA | NA | NA | 230 | 99.99 |
| EAS-P-2 | 17 | 98 | 151 | NA | NA | NA | 266 | 99.99 |
| EUR-P-1 | 21 | 405 | 604 | NA | NA | NA | 1030 | 99.97 |
| EUR-P-2 | 18 | 609 | 546 | NA | NA | NA | 1173 | 99.97 |
| AFA-1 | NA | NA | NA | 1 | 1 | 0 | 2 | 99.99 |
| AFA-2 | NA | NA | NA | 0 | 9 | 0 | 9 | 99.98 |
[i] Pipeline errors: Errors in proband assembly caused by phasing, read correction, or assembly mistakes. Coverage errors: Errors caused by low depth of coverage in either the proband or paternal capture. Sequence complexity errors: Homopolymer or simple repeat length discrepancies between the proband and paternal assemblies. Bionano discrepancies: Number of missing DLE-1 sites in MHC assembly. HLA sequence errors: Number of differences compared to Illumina HLA typing data. Microarray errors: Number of positions discordant with microarray typing after manual review. Total errors: Total errors across all sources. Assembly accuracy: For PGF, COX, and proband samples, the total accuracy of MHC assembly. For AFA, the accuracy across positions was queried by Bionano, HLA typing, and microarray genotyping.