Table 2. Relationships between average allele coverage, probability of detection, and the number of matching PCRs.
| Conventional | ||||||||||||||||
| Allele name | % reads | Probability of detection | PCR match | Pool match | f-r 100% | |||||||||||
| Lypa-MHCI*2 | 16.36 | 1 | 1 | 1 | 0(0/0) | |||||||||||
| Lypa-MHCI*4 | 7.78 | 0.94 | 0 | 0 | 1(1/0) | |||||||||||
| Lypa-MHCI*5 | 6.85 | 0.94 | 0 | 0 | 1(1/0) | |||||||||||
| Lypa-MHCI*11 | 3.23 | 0.86 | 1 | 1 | 0(0/0) | |||||||||||
| Lypa-MHCI*8 | 0.80 | 0.44 | 1 | 1 | 0(0/0) | |||||||||||
| Lypa-MHCI*7 | 0.36 | 0.17 | 0 | 0 | 1(0/1) | |||||||||||
| Lypa-MHCI*9 | 0.24 | 0.44 | 0 | 0 | 1(1/0) | |||||||||||
| Lypa-MHCI*6 | 0.13 | 0.06 | 0 | 0 | 3(0/3) | |||||||||||
| Lypa-MHCI*14 | 0.00 | 0.00 | 0 | 0 | 2(1/1) | |||||||||||
| Pooled-PCRs | ||||||||||||||||
| Allele name | % reads | Probability of detection | PCR match | Pool match | f1-r1 50% | f2-r1 16.6% | f1-r2 16.6% | f1-r3 16.6% | ||||||||
| Lypa-MHCI*4 | 15.97 | 1 | 2 | 0.67 | 0(0/0) | 2(2/0) | 1(0/1) | 0(0/0) | ||||||||
| Lypa-MHCI*9 | 4.86 | 1 | 2 | 0.67 | 0(0/0) | 2(2/0) | 1(0/1) | 0(0/0) | ||||||||
| Lypa-MHCI*11 | 3.90 | 1 | 2 | 0.67 | 0(0/0) | 1(1/0) | 1(0/1) | 0(0/0) | ||||||||
| Lypa-MHCI*8 | 3.47 | 1 | 2 | 0.67 | 0(0/0) | 1(1/0) | 1(0/1) | 0(0/0) | ||||||||
| Lypa-MHCI*2 | 2.34 | 0.83 | 1 | 0.17 | 3(3/0) | 0(0/0) | 5(3/2) | 5(3/2) | ||||||||
| Lypa-MHCI*5 | 1.39 | 1 | 0 | 0.00 | 1(1/0) | 2(2/0) | 2(1/1) | 1(1/0) | ||||||||
| Lypa-MHCI*6 | 1.06 | 0.94 | 1 | 0.17 | 3(0/3) | 4(1/3) | 4(0/4) | 0(0/0) | ||||||||
| Lypa-MHCI*7 | 0.84 | 0.94 | 1 | 0.17 | 1(0/1) | 2(1/1) | 2(0/2) | 0(0/0) | ||||||||
| Lypa-MHCI*14 | 0.00 | 0.00 | 0 | 0.00 | 4(3/1) | 3(2/1) | 5(3/2) | 4(3/1) | ||||||||
| Pooled-primers | ||||||||||||||||
| Allele name | % reads | Probability of detection | PCR match | Pool match | fa 45.5% | fb 18.2% | fc 18.2% | fd 9.1% | fe 9.1% | ra 41.7% | rb 16.7% | rc 8.3% | rd 8.3% | re 8.3% | rf 8.3% | rg 8.3% |
| Lypa-MHCI*4 | 6.00 | 1 | 1 | 1 | 3 | 4 | 0 | 2 | 2 | 0 | 2 | 3 | 1 | 1 | 1 | 2 |
| Lypa-MHCI*8 | 5.49 | 1 | 1 | 1 | 0 | 3 | 1 | 1 | 1 | 0 | 2 | 3 | 1 | 1 | 1 | 2 |
| Lypa-MHCI*7 | 4.31 | 1 | 1 | 1 | 0 | 3 | 1 | 1 | 1 | 1 | 3 | 2 | 0 | 2 | 2 | 3 |
| Lypa-MHCI*11 | 3.83 | 1 | 1 | 1 | 0 | 3 | 1 | 1 | 1 | 0 | 2 | 3 | 1 | 1 | 1 | 2 |
| Lypa-MHCI*5 | 2.72 | 1 | 1 | 1 | 1 | 4 | 2 | 0 | 2 | 0 | 2 | 3 | 1 | 1 | 1 | 2 |
| Lypa-MHCI*9 | 1.60 | 1 | 1 | 1 | 1 | 4 | 0 | 2 | 2 | 0 | 2 | 3 | 1 | 1 | 1 | 2 |
| Lypa-MHCI*6 | 1.51 | 1 | 1 | 1 | 0 | 3 | 1 | 1 | 1 | 3 | 5 | 0 | 2 | 4 | 4 | 4 |
| Lypa-MHCI*2 | 1.41 | 1 | 1 | 1 | 1 | 0 | 4 | 4 | 2 | 2 | 0 | 5 | 3 | 2 | 3 | 3 |
| Lypa-MHCI*14 | 0.00 | 0 | 0 | 0 | 3 | 4 | 4 | 4 | 2 | 1 | 3 | 4 | 2 | 2 | 2 | 3 |
For each allele for which genomic data of the flanking region is available, the average percentage of reads corresponding to each allele copy (%reads) is shown, as well as the number of independent PCRs perfectly matching the allele’s priming sequences (PCR-match), the number of perfectly matching PCRs weighted by their proportion in the sequencing pool (if the allele is perfectly matched by primers in all four PCRs it would be 1 (Pool match)). The following columns depict the primers used in each PCR followed by the proportion of their corresponding product in the final sequencing pool and the number of total mismatching bases for each allele (mismatches primer F / mismatches primer R); see S2 Table for further details. In the pooled-PCRs strategy primers used in separate PCRs complement each other, so that most alleles are perfectly matched in at least one independent PCR. Similarly, in the case of pooled-primers all alleles are perfectly matched by at least one of the non-degenerate primers used. Alleles not present in the genome assembly are not shown.