Table 2.

Average number of autosomal variants identified per animal using three sequence variant genotyping methods

	Full			Filtered
	GATK	Graphtyper	SAMtools	GATK	Graphtyper	SAMtools
Total biallelic SNPs	6,324,455	7,384,058	6,617,948	6,105,674	6,533,711	6,564,229
Heterozygous	3,890,351	4,758,297	4,187,882	3,744,336	4,074,011	4,147,033
Homozygous ALT	2,434,104	2,625,761	2,430,066	2,361,338	2,459,700	2,417,196
Ti/Tv	2.17	2.13	2.11	2.20	2.14	2.13
Total biallelic indels	693,697	767,261	1,007,420	691,765	697,637	960,218
Heterozygous	390,495	441,172	616,981	388,622	391,856	593,417
Homozygous ALT	303,202	326,089	390,439	303,143	305,781	366,801
Singletons	49,166	23,406	32,810	41,408	17,999	32,398

The number of variants is presented for the three tools evaluated before (Full) and after (Filtered) applying recommended filters to identify and exclude low quality variants