Skip to main content

Advertisement

Table 2 Characteristics of marker panels used in different populations.

From: Linkage disequilibrium reveals different demographic history in egg laying chickens

  Dataset I Dataset II
  BE WE BC WC
Total Number of SNPs 57'635 57'635 36'455 36'455
# SNPs monomorph 15'675 33'915 11'800 22'815
# SNPs ungenotyped 836 894 982 1'059
# SNPs with MAF < 5% 2'893 1'883 2'392 450
Genome coverage1 (Mb) 1031 1027 956 949
# SNPs in use 37'075 19'802 19'892 8'447
# common SNPs2 14653 6072
Mean adjacent marker spacing (kb) 27.8 51.8 48.0 112.3
Mean MAF 0.28 ± 0.13 0.34 ± 0.14 0.28 ± 0.21 0.24 ± 0.15
Mean observed heterozygosity 0.35 ± 0.15 0.34 ± 0.15 0.47 ± 0.21 0.37 ± 0.13
Mean expected heterozygosity 0.37 ± 0.12 0.36 ± 0.12 0.373 ± 0.12 0.36 ± 0.12
  1. 1Genome coverage after filtering
  2. 2Number of common SNPs in use between BE and WE, and between BC and WC
  3. 3Expected heterozygosity under the assumption that BC was a pure line, which is not the case