Table 1.

Number of different types of autosomal sequence variants detected in 49 Original Braunvieh cattle using three sequence variant genotyping methods (Full) and subsequent variant filtration based on commonly used criteria (Filtered)

	Full			Filtered
	GATK	Graphtyper	SAMtools	GATK	Graphtyper	SAMtools
Variants	21,140,196	20,262,913	20,668,459	19,761,679	17,679,155	18,871,549
SNPs	18,594,182	18,120,724	17,592,038	17,248,593	15,777,446	16,272,917
Not in dbSNP	1,387,781	1,505,586	882,575	867,838	564,326	570,901
Biallelic	18,347,962	18,053,396	17,528,249	17,111,806	15,730,153	16,218,714
Multi-allelic	246,220	67,328	63,789	136,787	47,293	54,203
Ti/Tv ratio	2.09	2.07	2.05	2.17	2.18	2.16
SNP array (%)
BovineHD	99.46	99.61	99.32	99.21	98.79	98.85
Bovine SNP50	99.14	99.26	99.12	98.91	98.87	98.90
Indels	2,478,489	2,044,585	3,076,421	2,445,766	1,826,808	2,598,632
Not in dbSNP	663,831	596,137	1,279,162	639,219	456,752	979,291
Biallelic	2,166,352	1,753,391	2,704,413	2,133,840	1,571,195	2,310,386
Multi-allelic	312,137	291,194	372,008	311,926	255,613	288,246
Insertion/Deletion	0.88	0.88	1	0.88	0.88	0.99
Complex variation	67,525	97,604	0	67,320	74,901	0