Table 2.

Number distribution of variants detected in each chromosome

Chr	SNP			Indel				Insertion			Deletion			CNV			Genes
	n a	Genes	Ratio (%)	Gain	Loss	Genes	Ratio (%)	n a	Genes	Ratio (%)	n a	Genes	Ratio (%)	NO.	Genes	Ratio (%)	n b
1	3632	662	30.00	3323	1321	1023	46.30	1420	516	23.36	1013	639	28.93	20	22	1.00	2209
2	2857	640	29.80	2284	922	904	42.10	859	361	16.81	575	491	22.87	10	11	0.51	2147
3	2065	482	33.40	2072	789	727	50.30	709	295	20.43	471	385	26.66	7	8	0.55	1444
4	1427	389	31.00	1430	550	547	43.60	637	266	21.21	456	335	26.71	9	10	0.80	1254
5	4764	369	31.50	3907	1507	540	46.10	576	239	20.39	411	290	24.74	8	9	0.77	1172
6	2490	635	32.70	2342	897	944	48.60	884	349	17.98	591	480	24.73	13	13	0.67	1941
7	2191	487	29.50	1785	769	632	38.30	771	280	16.96	526	358	21.68	11	12	0.73	1651
8	918	247	29.20	1161	442	422	49.80	518	227	26.80	390	269	31.76	8	9	1.06	847
9	2053	397	27.80	1701	668	560	39.20	738	293	20.53	540	353	24.74	6	6	0.42	1427
10	898	185	35.30	778	308	254	48.50	324	130	24.81	225	152	29.01	8	9	1.72	524
11	695	156	37.00	533	266	208	49.30	222	99	23.46	149	128	30.33	2	2	0.47	422
12	1408	392	34.20	1337	555	559	48.80	409	183	15.98	266	252	22.01	6	10	0.87	1145
13	1718	479	31.20	2045	804	717	46.70	1051	396	25.81	733	487	31.75	12	12	0.78	1534
14	2627	514	37.50	2369	963	717	52.30	1103	380	27.74	746	471	34.38	10	11	0.80	1370
15	1519	296	30.80	1228	532	445	46.40	562	221	23.02	398	266	27.71	10	11	1.15	960
16	642	154	34.70	642	285	225	50.70	339	122	27.48	234	146	32.88	4	4	0.90	444
17	3817	265	38.50	2892	1250	334	48.50	390	149	21.66	251	196	28.49	5	5	0.73	688
18	1023	195	38.10	817	315	248	48.40	352	121	23.63	241	147	28.71	2	3	0.59	512
X	739	169	15.10	1366	584	405	36.20	572	191	17.05	429	226	20.18	17	22	1.96	1120
Y	1	0	0.00	19	6	3	23.10	0	0	0.00	0	0	0.00	0	0	0.00	13
Total	37 484	7113	31.20	34 031	13 733	10 414	45.60	12 436	4818	21.11	8645	6071	26.60	168	189	0.83	22 824

^aNumber of identified variants within genic regions.

^bNumber of total genes contained in the Ensembl gene database of pig.