Table 1. Counts of chickens and SNPs remaining post filtering.

		BRO	BRO2a	BRO3	BRO3a	BRO3b	BEL	WEL
Founders	Males	58	–	50	26	24	12	8
	Females	17	–	9	4	5	40	38
	Total	123a	48	59	30	29	52	46
SNPs	Raw count	966 355	790 531	789 359	692 467	778 135	891 200	691 954
	MAFb	833 639	658 548	638 947	631 449	645 713	796 430	627 294
	HWEc	760 893	789 450	788 284	691 625	777 771	763 931	420 130
	Missingnessd	966 346	788 594	787 732	690 038	776 114	888 903	690 298
	Final count	630 435	655 905	636 535	628 382	643 554	667 605	354 737

Abbreviations: BEL, brown egg layers; BRO, broilers; HWE, Hardy–Weinberg equilibrium; MAF, minor allele frequency; SNP, single-nucleotide polymorphism; WEL, white egg layers.

^aSex data unavailable for BRO2 line.

^bMarkers with minor allele frequency <0.05 within the cohort excluded.

^cMarkers with Hardy–Weinberg equilibrium deviation P-value <0.001 within the cohort.

^dMarkers with >5% data missing excluded.