Table S1. All Candidate Selective Sweeps Identified in the Porcine Genome

Table S1. All candidate selective sweeps identified in the porcine genome.

Genomic interval a / n. winb / n. SNPsc / nMAJ / nMIN d / Hp e / -ZHp f / Gene overlap(s) g /
chr1:125.87-126.02 / 1 / 24 / 472/25 / 0.06 / 4.83 / [1] *04597 NP_001106154.1 AQP9
chr1:152.93-153.51 / 3 / 158 / 3968/307 / 0.03 / 5.37 / [1] *27232 FAM169B; *27431 : [4] *04811 PGPEP1L :
[5] *04811 PGPEP1L :
[6] *04812 NP_999337.1 IGF1R
chr1:158.07-158.73 / 7 / 431 / 10274/629 / 0.06 / 4.94 / [1] *19192 ; *04834 ; *04835 MAGEL2; *04836 MKRN3; *26997 :
[3] *04839 CHRNA7 :
[6] *04839 CHRNA7
chr1:159.31-159.53 / 2 / 72 / 1451/190 / 0.11 / 4.05 / [1] *26006 NP_001011505.1 KLF13 :
[3] *04840 OTUD7A :
[5] *04840 OTUD7A
chr1:161.45-161.83 / 4 / 429 / 5695/422 / 0.09 / 4.40 / [1] *04856 NFATC1; *04857 ATP9B; *04857 ATP9B :
[5] *04858 SALL3
chr1:164.84-165.41 / 5 / 283 / 6983/697 / 0.07 / 4.71 / [1] *04863 ; *18662 : [5] *04861 TSHZ1
chr1:165.49-166.12 / 6 / 391 / 8224/656 / 0.10 / 4.19 / [1] *04870 NP_001230636.1 CNDP2; *04869 CNDP1; *04875 CYB5_PIG CYB5A; *04874 C18ORF63; *04872 C18ORF55; *04873 FBXO15
chr1:168.61-169.27 / 7 / 399 / 9772/649 / 0.06 / 4.87 / [1] *04878 NP_001163989.1 SOCS6; *23069 ; *26815
chr1:170.57-170.77 / 1 / 46 / 3451/1059 / 0.10 / 4.21 / [4] *04884 TMX3 :
[5] *04884 TMX3
chr1:171.20-171.91 / 5 / 192 / 5033/336 / 0.08 / 4.65 / [1] *30586 5S_rRNA
chr1:172.36-172.79 / 3 / 169 / 4778/159 / 0.04 / 5.23
chr1:175.11-175.26 / 1 / 44 / 1732/202 / 0.11 / 4.16
chr1:175.41-175.82 / 3 / 128 / 3402/151 / 0.02 / 5.49 / [1] *04890 SERPINB2; *04893 VPS4B; *04894 SERPINB5; *04895 BCL2; *25727 ; *25744 KDSR :
[3] *04891 SERPINB7 :
[5] *04891 SERPINB7
chr1:175.82-176.27 / 5 / 351 / 7975/1043 / 0.03 / 5.33 / [1] *20464 U6; *04896 PHLPP1 :
[5] *25744 KDSR
chr1:176.33-176.98 / 7 / 341 / 7903/645 / 0.07 / 4.76 / [1] *04897 ZCCHC2; *21838 ; *04898 TNFRSF11A; *04898 TNFRSF11A; *04899 KIAA1468; *04901 PIGN
chr1:177.33-177.48 / 1 / 22 / 4435/773 / 0.09 / 4.39 / [4] *04903 CDH20 : [6] *04903 CDH20
chr1:177.62-178.91 / 11 / 854 / 19220/768 / 0.03 / 5.42 / [1] *18100 7SK; *04904 MC4R_PIG MC4R; *26454 NP_999312.1 PMAIP1 :
[4] *04907 CCBE1 :
[5] *04907 CCBE1
chr1:179.07-179.29 / 2 / 196 / 6323/568 / 0.11 / 4.13 / [1] *04908 LMAN1; *04909 CPLX4; *04910 RAX :
[3] *04907 CCBE1 :
[5] *04907 CCBE1; *04911
chr1:240.12-240.47 / 2 / 83 / 1793/124 / 0.11 / 4.05
chr1:245.55-245.97 / 4 / 348 / 7610/521 / 0.08 / 4.52 / [4] *05232 SMARCA2 :
[6] *05232 SMARCA2
chr1:250.97-251.12 / 1 / 137 / 7687/853 / 0.09 / 4.34
chr1:257.04-257.19 / 1 / 393 / 9765/1053 / 0.09 / 4.41 / [3] *05282 VPS13A; *05284 NP_001090987.1 GNA14 :
[5] *05282 VPS13A :
[6] *05284 NP_001090987.1 GNA14
chr1:258.09-258.24 / 1 / 75 / 2321/220 / 0.06 / 4.84
chr1:259.80-260.08 / 2 / 270 / 8530/1482 / 0.11 / 4.15 / [1] *21237 :
[6] *22532 ; *22532
chr1:260.23-260.38 / 1 / 248 / 5558/340 / 0.08 / 4.59
chr1:273.23-273.38 / 1 / 34 / 1121/137 / 0.11 / 4.09 / [1] *05401 CYLC2; *05401 CYLC2
chr1:298.87-299.37 / 3 / 202 / 4021/369 / 0.00 / 5.82 / [1] *05590 PSB7_PIG PSMB7; *05591 GPR144; *05591 GPR144; *05592 SF-1; *05589 NR6A1_PIG NR6A1; *05588 STF1_PIG NR5A1; *18834 ; *19719 NR_031534.1; ssc-mir-181b
[3] *05587 NEK6_PIG NEK6; *23876 :
[5] *05587 NEK6_PIG NEK6 :
[6] *23876
chr2:7.27-7.47 / 1 / 68 / 1065/219 / 0.11 / 4.15 / [1] *22687 NAA40; *13049 RCOR2; *13050 MARK2; *13050 MARK2 :
[3] *13048 C11ORF84 :
[6] *13048 C11ORF84
chr2:33.77-34.19 / 4 / 252 / 13089/2470 / 0.06 / 4.87
chr2:52.93-53.16 / 2 / 268 / 4185/341 / 0.10 / 4.29 / [1] *13410 SWAP70; *27581 :
[3] *13409 SBF2 :
[5] *13409 SBF2 :
[6] *22191
chr2:72.51-72.86 / 3 / 115 / 3675/645 / 0.10 / 4.19 / [1] *13562 ; *24580 ; *13559 ; *13559 ; *22228 ; *22228 ; *22380 SH2D3A; *13554 TRIP10; *13556 EMR1; *13552 GPR108; *13551 ; *21281 ; *13555 ; *13553 VAV1
chr3:78.46-78.61 / 1 / 244 / 11786/1641 / 0.10 / 4.18
chr4:28.35-28.70 / 2 / 322 / 6336/504 / 0.06 / 4.86
chr4:37.31-37.66 / 3 / 119 / 2508/211 / 0.11 / 4.06 / [1] *06056 ODFP1_PIG ODF1; *27480 NP_001127816.1 KLF10; *24130 ; *25427 ; *24504 ; *24200 :
[6] *06058 RRM2B
chr4:82.56-82.71 / 1 / 26 / 712/1 / 0.00 / 5.77 / [1] *06247 PLAG1; *06248 MOS_PIG MOS; *06249 RS20_PIG RPS20; *18353 snoU54 :
[4] *06246 CHCHD7 :
[6] *06246 CHCHD7; *06250 LYN
chr5:88.04-88.19 / 1 / 208 / 6499/970 / 0.05 / 5.06 / [1] *18270 U6; *00878 DEPDC4 :
[2] *26697 UHRF1BP1L :
[4] *25682 ACTR6; *23835 :
[5] *26697 UHRF1BP1L; *26697 UHRF1BP1L :
[6] *00877 SCYL2; *25682 ACTR6; *23835
chr5:89.80-89.95 / 1 / 32 / 2316/553 / 0.11 / 4.15
chr7:10.16-10.49 / 2 / 245 / 4826/360 / 0.10 / 4.25 / [1] *01056 RANBP9; *30526 SIRT5 :
[4] *01054 GFOD1 :
[6] *01054 GFOD1
chr7:103.27-103.42 / 1 / 43 / 901/178 / 0.05 / 5.08 / [1] *02363 VSX2 : [3] *27564 NP_001172765.1 LIN52; *02362
[5] *27564 NP_001172765.1 LIN52; *02359 :
[6] *02362
chr7:112.47-112.62 / 1 / 79 / 6313/1008 / 0.07 / 4.68
chr8:12.54-12.84 / 3 / 137 / 5872/401 / 0.03 / 5.29 / [1] *08747 NCAPG; *08748 NP_001182274.1 LCORL
chr8:45.31-45.61 / 2 / 264 / 8335/686 / 0.07 / 4.66 / [1] *08854 NP_001090908.1 CPE; *08855 :
[3] *08857 MSMO1_PIG SC4MOL :
[6] *08857 MSMO1_PIG SC4MOL
chr8:45.68-45.95 / 2 / 290 / 8670/928 / 0.08 / 4.63 / [1] *08858 KLHL2; *20868 TMEM192 :
[5] *08860
chr8:87.90-88.05 / 1 / 183 / 6521/1174 / 0.11 / 4.07 / [4] *09037 ZNF827 :
[5] *09037 ZNF827
chr8:132.83-132.98 / 1 / 29 / 6493/2282 / 0.11 / 4.15
chr9:53.55-53.70 / 1 / 121 / 3303/409 / 0.11 / 4.17 / [1] *28517 SC5DL :
[4] *26007 :
[5] *26007
chr9:109.84-110.04 / 1 / 22 / 701/76 / 0.09 / 4.44 / [1] *27203 ; *30638 :
[3] *15405 NP_001038087.1 CD36 :
[6] *15405 NP_001038087.1 CD36
chr9:129.79-130.02 / 2 / 256 / 6595/423 / 0.07 / 4.67 / [4] *15512 PAPPA2 : [5] *15512 PAPPA2
chr9:132.25-132.53 / 2 / 320 / 8181/878 / 0.10 / 4.21 / [1] *27614 ; *15523 RALGPS2; *25760 ; *15522 NP_001103417.1 ANGPTL1
chr9:149.43-149.58 / 1 / 157 / 4029/621 / 0.12 / 4.01 / [4] *15626 VWC2 :
[5] *15626 VWC2
chr10:45.57-45.77 / 1 / 103 / 2818/293 / 0.08 / 4.53
chr11:15.42-15.69 / 2 / 78 / 2449/284 / 0.08 / 4.63 / [1] *09370 NP_999179.2 FOXO1A
chr11:52.41-52.69 / 2 / 140 / 4631/862 / 0.05 / 5.01 / [1] *09466 UCHL3_PIG UCHL3
chr13:39.80-40.20 / 3 / 202 / 4192/304 / 0.10 / 4.19 / [3] *22522 :
[4] *27019 :
[5] *22522 ; *27019
chr13:122.53-122.81 / 2 / 163 / 6256/1765 / 0.11 / 4.08 / [3] *23871 NAALADL2 :
[5] *23871 NAALADL2
chr13:137.68-138.06 / 4 / 284 / 8737/509 / 0.03 / 5.32 / [1] *11815 NP_001092067.1 OSTN :
[4] *11817 CCDC50 :
[5] *11817 CCDC50
chr13:142.98-143.26 / 2 / 84 / 1687/125 / 0.10 / 4.18 / [1] *26934 PIGX; *21918 CEP19; *23527 LRRC33 : [4] *11843 PAK2; *11845 PCYT1A : [5] *11845 PCYT1A : [6] *11843 PAK2
chr13:146.66-146.81 / 1 / 73 / 3637/711 / 0.10 / 4.27 / [1] *24904 SEC22A :
[3] *27952 ADCY5 :
[5] *27952 ADCY5
chr13:208.25-208.60 / 3 / 237 / 4619/331 / 0.10 / 4.30 / [4] *12051 RUNX1 :
[6] *12051 RUNX1
chr15:115.76-116.28 / 5 / 342 / 5726/389 / 0.03 / 5.44 / [1] *16093 AOX1; *16099 FAM126B; *16098 ORC2; *16097 ; *25370 ; *28980 ORC2; *26143 ; *16100 NDUFB3; *16101 NP_001001628.1 FLIP-L; *26940 NP_001155112.1 CASP10; *16106 :
[4] *28157 CASP8 :
[5] *28157 CASP8 :
[6] *16094 NP_001231422.1 BZW1
chr15:122.82-122.97 / 1 / 164 / 7325/2032 / 0.06 / 4.86 / [1] *23264 IDH1 :
[4] *16146 C2ORF80; *16147 PIKFYVE :
[5] *16147 PIKFYVE :
[6] *16146 C2ORF80
chr16:52.42-52.57 / 1 / 34 / 3438/1388 / 0.10 / 4.24 / [1] *18684 :
[3] *16974 MAP1B; *23818 MRPS27 :
[5] *16974 MAP1B :
[6] *23818 MRPS27
chr16:58.41-59.06 / 6 / 515 / 13587/1077 / 0.07 / 4.75 / [1] *17010 FAM196B; *17011 CCDC99; *25965
chr18:5.20-5.48 / 2 / 131 / 3739/773 / 0.05 / 5.11 / [1] *16428 CCT8L2; *28615 ; *26577
chrX:49.64-51.70 / 18 / 1307 / 22074/962 / 0.03 / 3.56 / [1] *26529 ; *24298 ; *26105 ; *28863 ; *26271 ; *12316 CXORF67; *12317 GSPT2; *23120 U6; *12318 MAGD1_PIG MAGED1; *27932 ; *12319 ; *18305 SNORA11; *24958 GPR173; *12323 TSPYL2; *12322 KDM5C_PIG KDM5C; *12324 IQSEC2; *12324 IQSEC2 :
[3] *12325 SMC1A; *12325 SMC1A :
[5] *20269 U6; *12326 RIBC1 :
[6] *12325 SMC1A; *12325 SMC1A; *12327 HSD17B10
chrX:63.37-82.77 / 181 / 15761 / 270284/3422 / 0.00 / 3.91 / [1] *12382 IGBP1; *12381 DGAT2L6; *12380 NP_001231097.1 P2RY4; *12379 ARRC_PIG ARR3; *12378 PDZ11_PIG PDZD11; *12377 ; *12376 GDPD2; *12375 DLG3; *29962 ; *25388 ; *24346 NP_001124445.1 SLC7A3; *30084 ; *12400 SNX12; *12399 FOXO4; *12397 NP_999248.2 IL2RG; *12396 MED12; *28532 ; *12395 ; *12392 RHOG; *24163 ZMYM3; *12394 GJB1; *27465 NLGN3; *12403 OGT1_PIG OGT; *12401 ACRC; *12402 CXCR3; *12404 ; *27816 ; *20876 ; *12408 NHSL2; *23312 PIN4; *21834 ERCC6L; *20283 U6; *12406 ; *12405 NP_001191212.1 RPS4; *12409 NP_001033053.1 CITED1; *12410 HDAC8; *12411 PHKA1; *12411 PHKA1; *12411 PHKA1; *21200 ; *21233 ; *25063 ; *25063 ; *29204 ; *12415 NAP1L2; *23461 ; *21881 ; *21225 CDX4; *12416 CHIC1; *18627 ; *18359 ; *19255 ; *19673 ; *18719 ; *29458 ; *12419 RLIM; *20747 ; *28538 ; *21754 ; *25929 KIAA2022; *30499 ; *12424 ABCB7; *12425 NP_001230218.1 UPRT; *12426 ZDHHC15; *12427 ; *12430 ; *30577 CXorf26; *26464 ssc-mir-325; *18346 ; *12431 ; *26245 ssc-mir-325; *21054 ATRX; *29017 FGF16; *22833 FGF16; *12434 ; *12433 ATRX; *21554 ; *12435 MAGT1; *12437 ATP7A; *12441 ; *12439 PGK1; *26714 TAF9B; *26714 TAF9B; *12440 PGK1_PIG PGK1; *12443 CLTR1_PIG CYSLTR1; *24448 ZCCHC5; *12445 LPAR4; *12446 NP_001230606.1 P2RY10; *30020 GPR174; *21734 GPR174; *12448 NP_001026968.1 ITM2A; *25552 ; *12449 TBX22; *24178 ; *12450 FAM46D; *25156 BRWD3; *22100 ; *12452 SH3BGRL; *20977 SH3BGRL; *21589 ; *12454 POU3F4; *12455 CYLC1; *12456 RPS6KA6; *12458 ; *12459 APOOL; *23546 ; *24291 APOOL; *24291 APOOL; *21601 ZNF711; *12462 POF1B; *12463 CHM; *19895 ; *20102 U6; *21256 ; *29941 ; *12467 KLHL4; *12469 ; *12470 :
[5] *19658
chrX:82.84-101.49 / 191 / 18253 / 323286/3251 / 0.00 / 3.90 / [1] *27260 ; *29112 ; *12471 POL; *12473 ; *21788 ; *27012 ; *20584 SNORA18; *12474 DIAPH2; *22239 U6; *27552 ; *27250 ; *19498 U6; *20516 ; *24086 ; *27066 ; *12479 PCDH19; *12480 NP_001093404.1 TNMD; *12481 NM_001244061.1 TSPAN6; *12482 SRPX2; *28625 ; *12483 ; *12484 ; *12486 CSTF2; *12486 CSTF2; *12485 NOX1; *12487 XKRX; *12488 ARL13A; *12491 CENPI; *12490 TMEM35; *12490 TMEM35; *12489 TRMT2B; *12492 DRP2; *12493 TAF7L; *12494 TIMM8A; *12495 NP_001230505.1 BTK; *12507 ; *30628 ; *25009 ; *12504 NAP1L3; *18276 ; *12503 ; *26918 U6; *12502 ; *28955 ; *29771 PC11X_PIG PCDH11X; *12496 ; *12497 ; *20695 ; *20733 ; *12500 ; *12508 ARMCX6; *12509 ARMCX3; *12510 ARMCX2; *24956 ; *28913 ; *12512 ZMAT1; *12513 ; *28062 ; *12514 BEX5; *26976 ; *28825 ; *12516 ; *28695 TMSB15A; *12518 ; *12519 GPRASP1; *12521 GPRASP2; *12520 BHLHB9; *18490 U6; *12523 TCEAL8; *12524 ; *12525 ; *12526 TCEAL7; *12527 WBP5; *12528 NGFRAP1; *12529 ; *12530 NP_001230359.1 TCEAL4; *12531 ; *12532 TCEAL1; *12534 MORF4L2; *12535 GLRA4; *22571 ; *25890 RAB9B; *12536 MYPR_PIG PLP1; *21101 ; *12517 ; *12540 MCART6; *12541 ; *12543 ESX1; *12542 FAM199X; *12544 ; *26039 ; *25678 ; *22981 ; *22981 ; *12545 IL1RAPL2; *12546 ; *12547 THBG_PIG SERPINA7; *12548 MUM1L1; *12549 CXORF57 :
[6] *30419 ; *28130
chrX:102.10-102.25 / 1 / 24 / 1388/154 / 0.04 / 3.37
chrX:104.92-105.29 / 3 / 152 / 2901/171 / 0.03 / 3.49 / [1] *12578 ; *12580 GUCY2F; *12579 :
[5] *12581 NXT2
chrX:127.14-127.49 / 3 / 78 / 2540/708 / 0.05 / 3.33 / [1] *12699 NP_999540.1 FHL1C; *12700 MAP7D3; *12700 MAP7D3; *25753 BRS3 :
[3] *12698 SLC9A6 :
[4] *23062 HTATSF1 :
[5] *12698 SLC9A6; *23062 HTATSF1
*is used instead of ENSSSCG000000 for Ensembl Gene ID’s.
aChromosome and coordinates of region in Megabases, i.e. chromosome:start-end.
bNumbers of consecutive ZHP < -4 windows that were merged (one window with ZHp lower than -3 was allowed to bridge two windows both having ZHp lower than -4.
cNumbers of SNPs that were identified in region (for merged windows, the number is that of all windows).
dSums of major (nMAJ) and minor alleles (nMIN) observed at all SNPs in the region.
eThe lowest Heterozygosity observed for a window in the region.
fThe lowest Z-score of Heterozygosity observed for a window in the region.
gGene(s) overlapping putative sweep region: [1] = Gene contained within region. [2] = Region contained within gene(s). [3] Region overlaps 5’-end of gene(s). [4] = Region overlaps 3’-end of gene(s). [5] = the 5’- end of gene(s) is within 20 kb of region. [6] = the 3’-end of gene(s) is within 20 kb of region.