From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species

Table 2 Genotypic differences between loci common to the 3 pipelines for devils (155 loci) and geese (3283 loci). Concordance rates (identical genotype calls between samples) between pipelines are in parentheses. Discordant genotype calls are presented as the percent of total genotypes

Homozygous → Homozygous refers to those loci where an AA is called a TT in the other pipeline for example. Homozygous → Heterozygous are any genotype calls that are homozygous in the first pipeline but called heterozygous in the other for that sample at the same locus. Heterozygous → Homozygous are those calls that are heterozygous in one pipeline but called homozygous in the other for that sample at the same locus

ISSN: 1471-2164