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Table 1 Genomic regions containing the top 0.1% of SNP, ranked using a moving (5 SNP) average (WIN5) of –log 10 (combined Peddrift P-values)

From: Signatures of selection in sheep bred for resistance or susceptibility to gastrointestinal nematodes

Region Chr Position (Mb) SNP50 BeadChip SNP Top SNP Peak SNP Peak SNP rank FSTPeak PEDDRIFT WIN5 -log10(p-value) Genes Candidate gene(s) in region (OARv3.1)
Romney Perendale Romney Perendale Combined
1 1 66.74-67.43 14 4 s43910 5 0.1632 0.3901 0.6799 3.0134 2.5988 1  
2 1 87.38-88.13 10 3 OAR1_93166689 7 0.3475 0.1424 2.1441 1.3027 2.5124 18 CD53, CHI3L2, CHIA, DENND2D
3 3 78.72-79.32 12 3 s08153 11 0.4868 0.2270 1.7146 1.6205 2.4161 3  
4 3 98.12-98.51 9 4 OAR3_104545117_X 2 0.6897 0.1148 3.1276 0.7050 2.8569 0  
5 4 44.99-45.39 10 4 OAR4_47833230 10 0.2439 0.3645 0.6647 3.0036 2.4283 2 RELN
6 4 83.23-83.69 12 4 OAR4_88693058_X 20 0.4264 0.0256 2.9894 0.3238 2.2755 0  
7 5 95.21-95.69 11 3 OAR5_103935962 14 0.4816 0.0927 2.7849 0.6253 2.3464 2  
8 7 81.54-82.04 9 2 OAR7_89131104 15 0.3167 0.1509 1.8827 1.6553 2.3387 10  
9 8 41.02-41.48 11 1 OAR8_44326031_X 39 0.2327 0.4345 0.9548 2.1834 2.0028 1  
10 9 11.31-11.69 8 3 OAR9_11436829 26 0.3990 0.1750 1.8185 1.2966 2.1687 0  
11 9 66.27-67.09 13 2 OAR9_70612779 4 0.4586 0.1935 1.9607 1.6057 2.6214 0  
12 16 16.67-16.88 7 2 s59518 23 0.6775 0.1604 2.1737 0.9608 2.2246 2  
13 16 17.33-17.7 11 5 s61002 1 0.5391 0.0953 3.2562 0.7822 3.0273 0  
14 16 66.35-66.7 9 1 s54054 35 0.6238 0.0791 2.4545 0.4334 2.0232 4 NSUN2
15 19 54.68-55.19 9 1 OAR19_58095077 44 0.2582 0.2780 0.9065 2.1367 1.9812 3 HRH1
16 25 39.57-40.32 19 2 OAR25_41988307 31 0.5301 0.1371 2.5086 0.9984 2.0855 1  
  1. The top 5% of SNP were used to define the boundaries of each region (see Materials & Methods). Position is taken from build 3.1 of the sheep genome. The number of SNP50 BeadChip SNP and the number of top SNP (0.1%) are given in each region. Peak SNP is defined as the SNP with the lowest WIN5 –log10(combined Peddrift P-value) in the region, and the rank of that SNP is also shown. Maximum FST and –log10 (Peddrift P-value) are shown for each breed. The number of genes in each region, along with candidates (defined as those with a previously reported role in immunity) was taken from Ensembl release 74.