Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals

Table 6 Descriptive statistics of the genomic datasets after the genotype quality control

Breeds	N	SNP	Call rate	Duplicates	NA/SDP	Total 1	MAF	HWE	Total 2
ANG	99	46,989	260	0	0	46,729	10,399	19	36,311
ANGSIM	487	52,597	0	0	4014	48,583	9633	31	38,919
BOR	158	52,497	1315	0	0	51,182	16,525	161	34,496
BRM	70	46,989	1047	0	0	45,942	19,456	44	26,442
CGU	140	52,497	3435	0	0	49,062	10,428	130	38,504
CHL	62	46,989	401	0	0	46,588	9352	18	37,218
GIR	50	46,989	1260	0	0	45,729	24,289	33	21,407
HFD	61	46,989	252	0	0	46,737	8816	105	37,816
HOL	137	46,989	1350	0	0	45,639	9416	16	36,207
JER	84	46,989	1377	0	0	45,612	13,163	56	32,393
LMS	87	46,989	243	0	0	46,746	9925	37	36,784
MON	271	51,084	0	0	0	51,084	142	127	50,815
NEL 35	209	35,237	780	16	1624	32,817	2529	1385	28,903
NEL 50	192	54,791	942	9	3647	50,193	9895	1804	38,494
SEN	153	52,497	1633	0	0	50,864	12,635	91	38,138
SGT	55	46,989	619	0	0	46,370	9768	28	36,574

All breed abbreviations are defined in Table 5
N Number of animals used in the analyses, NA / SDP Non-autosomal SNPs or SNPs without defined positions, Total 1 Number of SNPs used for ROH and HER analyses, Total 2 Number of SNPs used in the inbreeding and effective population size analyses performed, MAF Lower allele frequency, HWE Hardy-Weinberg equilibrium

ISSN: 1471-2164