Summary statistics of sequence variation data for individual LHB/CGB genes and predicted hotspot region
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Haplotypesh |
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| Analyzed region
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Segregating sites (S)
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MSVd |
MAF ≥10%
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Length (bp)
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GC %
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Pa |
All
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≥10% MAFc |
Singletons
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Type 1
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Type 2
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%
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SNPs in dbSNP
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πe |
θf |
Dg |
All No.
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No.
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Carriers (%)
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| Individual genes | ||||||||||||||||||||||||
| LHB | 1541 | 63 | E | 20 | 15 | 2 | 0 | 7 | 35.0 | 12 | 0.00371 | 0.00254 | 1.35 | 14 | 2 | 65.9 | ||||||||
| H | 17 | 10 | 1 | 0 | 6 | 35.3 | 12 | 0.00348 | 0.00246 | 1.28 | 7 | 2 | 84 | |||||||||||
| M | 20 | 10 | 5 | 1 | 7 | 40.0 | 11 | 0.00313 | 0.00295 | 0.20 | 16 | 2 | 50 | |||||||||||
| All | 27 | 8 | 1 | 10 | 55.0 | 12 | 0.00375 | 0.00301 | ||||||||||||||||
| CGB | 1543 | 64 | E | 18 | 14 | 2 | 7 | 72.2 | 2 | 0.00406 | 0.00228 | 2.24* | 15 | 2 | 74.5 | |||||||||
| H | 20 | 16 | 2 | 8 | 8 | 80.0 | 2 | 0.00530 | 0.00304 | 2.39* | 13 | 2 | 72 | |||||||||||
| M | 28 | 23 | 3 | 10 | 13 | 82.1 | 5 | 0.00666 | 0.00413 | 2.06* | 14 | 3 | 60.8 | |||||||||||
| All | 35 | 6 | 11 | 16 | 77.1 | 5 | 0.00545 | 0.00401 | ||||||||||||||||
| CGB2 | 1521 | 63 | E | 8 | 4 | 2 | 2 | 3 | 62.5 | 2 | 0.00115 | 0.00103 | 0.29 | 10 | 4 | 92.6 | ||||||||
| H | 12 | 3 | 6 | 2 | 6 | 66.7 | 2 | 0.00101 | 0.00176 | -1.26 | 8 | 3 | 80 | |||||||||||
| M | 24 | 4 | 10 | 2 | 9 | 45.8 | 2 | 0.00237 | 0.00359 | -1.12 | 12 | 2 | 56.5 | |||||||||||
| All | 34 | 15 | 5 | 13 | 52.9 | 2 | 0.00145 | 0.00384 | ||||||||||||||||
| CGB1 | 1510 | 63 | E | 5 | 4 | 0 | 0 | 1 | 20.0 | 1 | 0.00095 | 0.00065 | 0.99 | 6 | 3 | 82.9 | ||||||||
| H | 12 | 4 | 5 | 2 | 1 | 25.0 | 1 | 0.00119 | 0.00177 | -0.98 | 8 | 3 | 78 | |||||||||||
| M | 14 | 5 | 3 | 2 | 2 | 28.6 | 1 | 0.00157 | 0.00226 | -0.95 | 9 | 3 | 75.9 | |||||||||||
| All | 20 | 5 | 2 | 5 | 35.0 | 1 | 0.00124 | 0.00239 | ||||||||||||||||
| CGB5 | 1661 | 64 | E | 13 | 7 | 2 | 0 | 8 | 61.5 | 2 | 0.00155 | 0.00153 | 0.03 | 15 | 2 | 73.4 | ||||||||
| H | 13 | 6 | 5 | 1 | 5 | 46.2 | 2 | 0.00117 | 0.00175 | -0.99 | 9 | 2 | 78 | |||||||||||
| M | 13 | 10 | 1 | 2 | 8 | 76.9 | 2 | 0.00213 | 0.00178 | 0.59 | 11 | 4 | 78.3 | |||||||||||
| All | 25 | 7 | 2 | 13 | 60.0 | 2 | 0.00165 | 0.00259 | ||||||||||||||||
| CGB7 | 2233 | 63 | E | 30 | 27 | 1 | 6 | 6 | 40.0 | 4 | 0.00552 | 0.00271 | 3.18** | 31 | 2 | 47.8 | ||||||||
| H | 29 | 27 | 0 | 4 | 10 | 48.3 | 4 | 0.00484 | 0.00300 | 2.04* | 16 | 2 | 52 | |||||||||||
| M | 41 | 25 | 1 | 8 | 13 | 51.2 | 5 | 0.00429 | 0.00418 | 0.09 | 21 | 2 | 45.6 | |||||||||||
| All | 50 | 1 | 9 | 14 | 46.0 | 5 | 0.00550 | 0.00385 | ||||||||||||||||
| Predicted recombination hotspot regionb | ||||||||||||||||||||||||
| All region | 8338 | 56 | E | 64 | 42 | 14 | 0.00212 | 0.00196 | 0.32 | |||||||||||||||
| Intergenic CGB5/8 | 1879 | 52 | E | 17 | 12 | 2 | 0.00257 | 0.00219 | 0.61 | |||||||||||||||
| CGB8 | 2156 | 62 | E | 15 | 6 | 7 | 1 | 5 | 42.9 | 6 | 0.00152 | 0.00178 | -0.54 | 10 | 3 | 50 | ||||||||
| Intergenic CGB8/7
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4303
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54
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E
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32
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24
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5
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0.00227
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0.00208
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0.35
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19
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↵a (E) Estonians (n=47); (H) Han (n=25); (M) Mandenka (n=23).
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↵b Data for CGB8 are from 11 Estonian individuals from the resequencing of potential recombination hotspot (see text for explanation).
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↵c (MAF) Minor allele frequency.
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↵d Multisite variation (Fredman et al. 2004): (MSV1) SNPs that are also represented as paralogous sequence variants (PSVs) among the duplicons. (MSV2) SNPs present in >1 duplicated gene.
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↵e Estimate of nucleotide diversity per site from average pairwise difference among individuals.
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↵f Estimate of nucleotide diversity per site from number of segregating sites (S).
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↵g Significance level of Tajima's D statistics: (**) p < 0.01; (*) p < 0.05.
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↵h Haplotype distribution is the estimate by PHASE algorithm (Stephens et al. 2001).
