Table 1 PLINK parameters for run of homozygosity (ROH) analysis
From: Identification of selection signatures involved in performance traits in a paternal broiler line
Parameter | Value | Definition |
|---|---|---|
-homozyg-snp | 50 | Minimum number of SNP required to consider a ROH; |
-homozyg-kb | 300 | Size (Kb) of the sliding window; |
-homozyg-density | 50 | Minimum density required to consider a ROH; |
-homozyg-gap | 1000 | Maximum size (Kb) between two SNP to be considered in the same ROH; |
-homozyg-window-snp | 50 | Number of SNP present in the sliding window; |
-homozyg-window-het | 3 | Number of heterozygous SNP allowed in a ROH; |
-homozyg-window-missing | 5 | Number of missing calls allowed in a ROH; |
-homozyg-window-threshold | 0.05 | Proportion of overlapping windows that must be called homozygous to define a given SNP as in a homozygous segment. |