Table 5.
MHC haplotype coverage
| Haplotype | MHC length | MHC assembly length | Coverage with RCCX CNV (%) | Estimated RCCX length | Coverage without RCCX CNV (%) |
|---|---|---|---|---|---|
| PGF | 3,666,139a | 3,603,019 | 98.28 | 63,120 | 100.00 |
| COX | 3,590,884a | 3,560,067 | 99.14 | 24,160 | 99.81 |
| EAS-P-1 | 3,556,161b | 3,466,357 | 97.47 | 89,804 | 100.00 |
| EAS-P-2 | 3,752,278b | 3,668,815 | 97.78 | 83,463 | 100.00 |
| EUR-P-1 | 3,665,951b | 3,600,868 | 98.22 | 64,783 | 99.99 |
| EUR-P-2 | 3,623,607b | 3,559,803 | 98.24 | 63,504 | 99.99 |
| AFA-1 | 3,745,027b | 3,687,868 | 98.47 | 57,159 | 100.00 |
| AFA-2 | 3,624,487b | 3,567,034 | 98.41 | 57,453 | 100.00 |
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MHC assembly length is the sum of the contig lengths generated by the MHC assembly pipeline. The majority of the missing coverage is across the RCCX CNV which was omitted from the assembly. The RCCX CNV length and layout were estimated from the Bionano optical maps.
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aMHC length is known.
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bMHC length is estimated using Bionano optical maps.
