. 2019 Jan 11;9:728. doi: 10.3389/fgene.2018.00728

Table 2.

Functional annotation of the detected SNPs and indels.

		Eastern Finncattle	Western Finncattle	Yakutian cattle
SNP	Total number of SNPs	11,017,215	10,543,290	12,242,166
	Intergenic	7,998,914	7,662,604	8,845,911
	Intronic	2,764,951	2,643,821	3,114,622
	Exonic^a
	Non-synonymous	30,982	28,733	32,782
	Stop gain	294	284	310
	Stop loss	23	18	19
	Synonymous	41,111	38,137	46,950
	Upstream	74,552	69,369	82,170
	Downstream	74,198	70,815	83,549
	Upstream; downstream^b	1,636	1,534	2,036
	UTR^c	25,545	23,342	28,273
	Splicing	417	388	459
	ncRNA	4,593	4,256	5,086

Indel	Total number of indels	1,275,128	1,188,892	1,374,577
	Intergenic	942,143	878,007	1,012,733
	Intronic	332,504	310,089	363,783
	Exonic^a
	Non-frameshift	397	327	427
	Stop gain	24	22	27
	Stop loss	1	1	0
	Frameshift	1,045	972	1,148
	Upstream	9,269	8,286	9,861
	Downstream	10,611	9,609	11,377
	Upstream; downstream^b	250	218	282
	UTR^c	3,380	3,101	3,767
	Splicing	248	233	268
	ncRNA	406	371	437

^aExonic = “exonic” and “exonic; splicing” as annotated by ANNOVAR. ^bUpstream; downstream = variant located in downstream and upstream regions. ^cUTR = “UTR3” and “UTR5” as annotated by ANNOVAR.