Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage

Table 1 Counts of variants per chromosome

Chromosome	Biallelic	Triallelic	InDels
1	953,116	1,594	106,808
2	765,523	1,540	86,271
3	689,653	1,061	74,819
4	727,730	1,059	81,188
5	711,291	1,236	78,518
6	715,956	1,306	81,170
7	647,618	944	72,861
8	662,730	929	73,740
9	605,302	884	69,531
10	628,109	968	68,543
11	594,105	1,102	64,693
12	658,305	1,117	70,418
13	467,872	977	50,653
14	496,824	852	54,644
15	563,600	736	60,307
16	479,831	785	52,312
17	454,188	722	51,040
18	378,391	604	40,948
19	370,300	787	39,877
20	449,443	744	49,207
21	410,810	612	44,478
22	335,787	520	36,763
23	420,876	676	42,587
24	371,270	632	40,919
25	269,464	430	27,099
26	316,133	507	34,077
27	287,872	470	32,574
28	290,731	482	31,154
29	350,281	665	36,219
X (non PAR)	285,956	486	44,949
X (PAR)	79,554	119	8,253

Multi-sample variant calling was performed as described in Methods. The X chromosome was divided into a pseudoautosomal region (PAR) and a non-pseudoautsomal region (PAR) (see Additional file 9).

ISSN: 1471-2164