Most of the 1059 “Fowlers Pit” individuals were genotyped towards the 4553 SNPs within IKMB within Kiel School

Most of the 1059 “Fowlers Pit” individuals were genotyped towards the 4553 SNPs within IKMB within Kiel School

Personal genotyping and you may quality assurance

Quality control was done using the R package GWASTools (v1.6.2) and details are provided in Knief et al. . In summary, we removed 111 individuals with a missing call rate larger than 0.05 (which was due to DNA extraction problems, but these birds were genotyped in the follow-up study; see the “Follow-up genotyping and phenotyping in captive populations” section below), leaving 948 individuals. Further, we removed 152 SNPs that did not form defined genotype clusters, or had high missing call rates (missing rate >0.1), or were monomorphic, or deviated strongly from HWE (Fisher’s exact test P < 0.), or because their position in the zebra finch genome assembly was likely not correct, leaving 4401 SNPs. (more…)

Continue ReadingMost of the 1059 “Fowlers Pit” individuals were genotyped towards the 4553 SNPs within IKMB within Kiel School