Table 1. Classification and descriptive statistics of all 59 PERVs in the Sus scrofa reference genome (assembly Build 11.1) .

No.	Category1	Subclass	PERV name	Chromosome / unplaced contig	Strand	Position	Length2	Unique k-mer3	Detection rate4
1: LcPERV indicates long and complete or near-complete PERV; siPERV indicates short incomplete PERV. 2: The pol gene of sPERV-JX3like-15-116.3M was inserted by a 6 302 bp long sequence containing LINE1 transposon and (T)n simple repeat, which resulted in the length of the PERV increasing to 13 105 bp. 3: The number of unique k-mer (k=31) of PERV on pig reference genome. 4: The detection proportion of the PERV in the 63 Chinese and Western pigs; since the PERV sPERV-Clike-Y-25.29M has no unique k-mers, it cannot be detected in the tested pigs. /: Not available.
1	lcPERV	PERV-A	PERV-A-1-132.0M	1	+	132020281–132028361	8 081	253	0.57
2	lcPERV	PERV-A	PERV-A-1-262.2M	1	+	262166347–262175262	8 916	35	0.38
3	lcPERV	PERV-A	PERV-A-3-10.6M	3	−	10660619–10669533	8 915	647	0.24
4	lcPERV	PERV-A	PERV-A-5-92.1M	5	−	92185133–92194050	8 918	226	0.56
5	lcPERV	PERV-A	PERV-A-7-105.7M	7	+	105710884–105719193	8 310	119	0.17
6	lcPERV	PERV-A	PERV-A-8-51.6M	8	+	51570546–51579460	8 915	466	0.94
7	lcPERV	PERV-A	PERV-A-12-28.2M	12	+	28221374–28230287	8 914	95	0.43
8	lcPERV	PERV-A	PERV-A-13-142.0M	13	−	142030847–142039759	8 913	451	1
9	lcPERV	PERV-A	PERV-A-13-146.7M	13	−	146750532–146759521	8 990	520	1
10	lcPERV	PERV-A	PERV-A-15-66.8M	15	−	66864153–66873044	8 892	500	0.44
11	lcPERV	PERV-A	PERV-A-17-3.7M	17	−	3794010–3802709	8 700	411	1
12	lcPERV	PERV-A	PERV-A-17-33.1M	17	+	33062883–33071800	8 918	930	0.41
13	lcPERV	PERV-Alike	PERV-Alike-U965-14.7kb	NW_018084965	+	14674–22827	8 154	1 933	0
14	lcPERV	PERV-A	PERV-A-U136-0.5M	NW_018085136	−	563793–572725	8 933	1 205	0.86
15	lcPERV	PERV-A	PERV-A-X-73.7M	X	−	73752986–73761903	8 918	577	0.51
16	lcPERV	PERV-A	PERV-A-Y-20.1M	Y	−	20194782–20203572	8 791	983	0.46
17	lcPERV	PERV-A	PERV-A-Y-21.8M	Y	−	21867301–21876035	8 735	920	0.38
18	lcPERV	PERV-A	PERV-A-Y-25.2M	Y	+	25245606–25253905	8 300	11	0.63
19	lcPERV	PERV-B	PERV-B-3-51.1M	3	−	51108601–51117360	8 760	197	0.86
20	lcPERV	PERV-B	PERV-B-4-45.5M	4	−	45599494–45608252	8 759	132	0.62
21	lcPERV	PERV-B	PERV-B-8-15.3M	8	+	15319428–15328187	8 760	177	0.76
22	lcPERV	PERV-B	PERV-B-9-138.8M	9	−	138895584–138904340	8 757	51	0.46
23	lcPERV	PERV-B	PERV-B-11-38.2M	11	+	38201361–38210116	8 756	386	0.86
24	lcPERV	PERV-B	PERV-B-14-119.7M	14	+	119667621–119676299	8 679	486	0.46
25	lcPERV	PERV-B	PERV-B-15-110.9M	15	−	110958945–110967782	8 838	374	0.44
26	lcPERV	PERV-B	PERV-B-16-59.6M	16	+	59571885–59580646	8 762	141	0.44
27	lcPERV	PERV-B	PERV-B-U086-42.1kb	NW_018085086	−	42158–50876	8 719	564	0.81
28	lcPERV	PERV-B	PERV-B-U255-1.9kb	NW_018085255	+	1949–10743	8 795	242	0.54
29	lcPERV	PERV-B	PERV-B-U331-13.8kb	NW_018085331	+	13836–22597	8 762	85	0.87
30	lcPERV	PERV-C	PERV-C-14-62.5M	14	−	62550397–62557645	7 249	652	0.78
31	lcPERV	PERV-JX1	PERV-JX1-7-21.2M	7	+	21236160–21244976	8 817	1 387	1
32	lcPERV	PERV-JX1	PERV-JX1-17-41.4M	17	−	41467519–41476101	8 583	1 343	1
33	lcPERV	PERV-JX1	PERV-JX1-U293-0.8M	NW_018085293	+	820148–829192	9 045	2 015	1
34	lcPERV	PERV-JX2	PERV-JX2-X-71.4M	X	+	71402222–71409912	7 691	1 472	0.49
35	lcPERV	PERV-JX3	PERV-JX3-3-17.8M	3	+	17778858–17788086	9 229	1 460	1
36	lcPERV	PERV-JX4	PERV-JX4-2-76.6M	2	−	76648002–76655788	7 787	859	1
37	siPERV	PERV-A	sPERV-A-6-10.4M	6	+	10402614–10407657	5 044	20	0.57
38	siPERV	PERV-A	sPERV-A-X-55.1M	X	+	55079139–55083211	4 073	168	0.86
39	siPERV	PERV-B	sPERV-B-1-38.5M	1	+	38459013–38465006	5 994	61	0.48
40	siPERV	PERV-B	sPERV-B-X-112.8M	X	−	112842765–112847657	4 893	108	0.76
41	siPERV	PERV-C	sPERV-C-5-29.4M	5	+	29356367–29361638	5 272	639	0.78
42	siPERV	PERV-C	sPERV-C-11-29.1M	11	−	29084884–29090328	5 445	611	0.57
43	siPERV	PERV-C	sPERV-C-13-146.75M	13	−	146759522–146764990	5 469	19	0.56
44	siPERV	PERV-C	sPERV-C-13-146.76M	13	−	146764392–146769858	5 467	34	0
45	siPERV	PERV-C	sPERV-C-X-81.5M	X	−	81543240–81545899	2 660	178	0.56
46	siPERV	PERV-Alike	sPERV-Alike-U293-0.9M	NW_018085293	+	909902–914028	4 127	729	0
47	siPERV	PERV-Clike	sPERV-Clike-U154-3.2kb	NW_018085154	+	3178–6483	3 306	505	0
48	siPERV	PERV-Clike	sPERV-Clike-U193-4.0kb	NW_018085193	+	3949–7250	3 302	232	0.57
49	siPERV	PERV-Clike	sPERV-Clike-U355-19.3kb	NW_018085355	+	19304–23938	4 635	604	0.81
50	siPERV	PERV-Clike	sPERV-Clike-Y-25.269M	Y	−	25269797–25273827	4 031	16	0.24
51	siPERV	PERV-Clike	sPERV-Clike-Y-25.29M	Y	−	25299007–25302057	3 051	0	/
52	siPERV	PERV-JX2like	sPERV-JX2like-12-23.0M	12	−	22986893–22991220	4 328	704	1
53	siPERV	PERV-JX3like	sPERV-JX3like-15-116.3M	15	+	116321677–116334781	13 105	1 206	1
54	siPERV	PERV-JX3like	sPERV-JX3like-17-9.5M	17	−	9536784–9541504	4 721	854	1
55	siPERV	PERV-JX3like	sPERV-JX3like-X-72.2M	X	+	72244018–72249170	5 153	907	0.49
56	siPERV	PERV-UC	sPERV-UC1-9-63.2M	9	−	63235598–63238136	2 539	405	0.63
57	siPERV	PERV-UC	sPERV-UC2-13-21.3M	13	+	21308535–21310732	2 198	422	0.78
58	siPERV	PERV-UC	sPERV-UC3-Y-24.4M	Y	+	24407502–24411155	3 654	644	0.24
59	siPERV	PERV-UC	sPERV-UC4-Y-25.261M	Y	+	25261084–25264796	3 713	728	0.16