Table 1.

Results from genotyping eight bluethroats at MHC class I exon 3 (MHCI), using two primer strategies (single index [SI] and dual index [DI]) on Ion Torrent

	MHCI‐SI	MHCI‐DI
Modified pipeline from Sommer et al. (2013)
Reads per amplicon after jMHC (including only variants with ≥3 reads within any amplicon)	8,744–48,840	2,953–18,154
Total number of alleles	18	18
Alleles per individual	6.6 (5–8)	6.6 (5–8)
Unique amino acid sequences	14	14
Errors in pedigree	0	0
AmpliSAS
Reads per amplicon	>5,000	3,002–>5,000
Reads per amplicon assigned to alleles	2,797–3,534	2,028–4,815
Total number of alleles	16	16
Alleles per individual	5.4 (4–7)	5.0 (4–7)
Alleles per amplicon	5.6 (4–7)	5.5 (4–8)
Unique amino acid sequences	13	13
Errors in replicates	3.4%	9.1%
Errors in pedigree	0	0

The datasets were genotyped through two pipelines; one using a modification of the pipeline published by Sommer et al. (2013) and one using the online tool AmpliSAS (Sebastian et al., 2016).