Table 1.

Number of SNPs before and after imputation with different filterings from GBS to WGS data.

Breed	Chromosome	Before imputation	After imputation
			Before filtering	After filtering (R 2 >0.3)	After filtering (R 2 >0.8)
Landrace pig	1	33,648	1,163,674	411,803	200,693
2	23,549	1,056,375	348,556	151,185
3	19,115	741,850	283,255	132,967
4	19,438	677,120	270,867	131,240
5	15,492	613,081	184,337	84,815
6	19,724	821,252	285,405	129,414
7	19,812	724,764	268,144	123,498
8	20,814	784,755	287,282	128,842
9	20,455	856,362	298,509	128,612
10	15,627	633,875	226,590	103,204
11	13,703	491,636	180,753	84,277
12	9,776	443,666	133,030	56,870
13	24,232	924,908	332,499	155,654
14	19,558	859,867	307,671	157,568
15	17,278	672170	211,950	97,611
16	13,863	551,359	215,034	105v006
17	10,879	486,742	138,882	58,702
18	8,594	332,521	130,367	63,620
Large White pig	1	33,648	1,258,467	575,618	274,460
2	23,549	1,001,874	362,988	151,533
3	19,115	755,528	304,432	131,781
4	19,438	693,446	341,445	166,814
5	15,492	627,469	260,109	115,518
6	19,724	884,061	337,922	139,947
7	19,812	785,970	304,112	130,640
8	20,814	803,550	352,306	154,089
9	20,455	782,655	351,867	162,192
10	15,627	669,065	242,483	93,945
11	13,703	579,287	242,877	102,102
12	9,776	465,664	166,687	67,556
13	24,232	1,007,593	461,286	226,507
14	19,558	836,804	385,503	185,524
15	17,278	658,978	289,207	132,518
16	13,863	540,903	225,310	90,049
17	10,879	467,065	182,444	75,628
18	8,594	326,200	146,694	67,842