Table 1 Criteria for filtering loci and genotypes. Filter steps that included a vizualiztion for setting thresholds are labled with a letter that corresponds to Figure 2. Unlabled filter steps did not require a visualiztion
FilterLociGenotypes% missingCriteria
ACoverage Per Base in Ref. Genome89,5737,264,9969.88Pre-genotyping filter (very low and high cov.)
BLocus Read Count Ratio71,7625,817,1639.93Allelic bias > than 6/1 removed
CLocus Total Coverage39,0303,465,3231.35Removed markers > 1400 and < 320 reads
DGenotype Coverage39,0301,972,37443.85Genotypes < 8 and > than 40 reads to missing
EGenotype Read Count Ratio39,0301,944,17444.65Allele bias in heterozygotes > (−/+ 3.26 log2)
FLocus Missing Genotypes24,2271,478,99132.17Removed loci with fewer than 50/90 genotypes
Correct Allelic Dropout24,2271,478,99132.17Impossible genotypes corrected
Segregation Distortion20,0931,226,28232.19Binom/chi square to remove segregation distortion
Parent-Offspring Match19,9281,216,60132.17ML cross-type of offspring ≠ parents