Table 2.
Results from genotyping eight bluethroats at MHC class II exon 2 (MHCII), using two primer strategies (single index [SI] and dual index [DI]) on Ion Torrent as well as being sequenced on Illumina MiSeq
| MHCII‐SI | MHCII‐DI | MHCII‐MiSeq | |
|---|---|---|---|
| Modified pipeline from Sommer et al. (2013) | |||
| Reads per amplicon after jMHC (including only variants with ≥3 reads within any amplicon) | 6,495–19,886 | 14,777–68,524 | 2,436–10,553 |
| Total number of alleles | 96 | 74 | 105 |
| Alleles per individual | 35.6 (29–47) | 23.0 (17–31) | 32.6 (23–41) |
| Unique amino acid sequences | 84 | 65 | 93 |
| Errors in pedigree | 2.1% | 4.3% | 3.4% |
| AmpliSAS | |||
| Reads per amplicon | >5,000 | >5,000 | 2,877–>5,000 |
| Reads per amplicon assigned to alleles | 3,251–4,445 | 3,754–4,681 | 2,611–4,721 |
| Total number of alleles | 75 | 74 | 94 |
| Alleles per individual | 27.8 (20–39) | 22.0 (16–30) | 27.8 (21–34) |
| Alleles per amplicon | 31.6 (22–42) | 23.5 (16–31) | 28.5 (21–35) |
| Unique amino acid sequences | 68 | 64 | 82 |
| Errors in replicates | 12.1% | 6.4% | 8.4% |
| Errors in pedigree | 6.4% | 10.9% | 12.5% |