Linkage disequilibrium reveals different demographic history in egg laying chickens

BMC Genomic Data

Table 2 Characteristics of marker panels used in different populations.

	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

¹Genome coverage after filtering
²Number of common SNPs in use between BE and WE, and between BC and WC
³Expected heterozygosity under the assumption that BC was a pure line, which is not the case

ISSN: 2730-6844