Table 2 Individual variant load in coding regions.
From: Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals
Variant type | Population | Very-rare (<0.1%) | Rare (0.1–0.5%) | Low (0.5–5%) | Common (>5%) | Total | |||||
---|---|---|---|---|---|---|---|---|---|---|---|
Mean | s.d. | Mean | s.d. | Mean | s.d. | Mean | s.d. | Mean | s.d. | ||
Heterozygous | |||||||||||
HGMD-DM* | 1KJPN (1,070) high confidence | 0.640 | 0.814 | 1.039 | 1.016 | 4.757 | 2.246 | 3.179 | 1.604 | 9.619 | 3.032 |
1KJPN (1,070) high-sensitive | 0.675 | 0.848 | 1.107 | 1.051 | 4.905 | 2.261 | 4.388 | 1.787 | 11.074 | 3.136 | |
1KGP JPT (89) | NA | NA | NA | NA | 6.270 | 2.503 | 4.169 | 1.829 | 10.438 | 2.969 | |
1KGP CHB (97) | NA | NA | NA | NA | 5.536 | 2.381 | 4.464 | 1.921 | 10.000 | 3.218 | |
1KGP CHS (100) | NA | NA | 1.470 | 1.359 | 4.320 | 2.049 | 3.680 | 1.803 | 9.470 | 2.798 | |
Stop-gained† | 1KJPN (1,070) high-confidence | 2.385 | 1.550 | 1.563 | 1.294 | 8.679 | 2.486 | 29.017 | 4.327 | 41.644 | 5.358 |
1KJPN (1,070) high-sensitive | 2.624 | 1.616 | 1.777 | 1.376 | 6.008 | 2.402 | 42.125 | 4.878 | 52.535 | 5.795 | |
1KGP JPT (89) | NA | NA | NA | NA | 8.685 | 2.987 | 39.337 | 5.261 | 48.022 | 6.166 | |
1KGP CHB (97) | NA | NA | NA | NA | 9.742 | 3.215 | 37.845 | 5.593 | 47.588 | 6.777 | |
1KGP CHS (100) | NA | NA | 3.860 | 2.433 | 6.580 | 3.085 | 36.070 | 4.860 | 46.510 | 5.947 | |
Homozygous | |||||||||||
HGMD-DM* | 1KJPN (1070) high-confidence | 0.001 | 0.031 | 0.003 | 0.053 | 0.048 | 0.230 | 1.570 | 1.126 | 1.621 | 1.145 |
1KJPN (1,070) high-sensitive | 0.000 | 0.000 | 0.003 | 0.053 | 0.050 | 0.234 | 1.862 | 1.235 | 1.914 | 1.251 | |
1KGP JPT (89) | NA | NA | NA | NA | 0.022 | 0.149 | 1.899 | 1.244 | 1.921 | 1.227 | |
1KGP CHB (97) | NA | NA | NA | NA | 0.052 | 0.222 | 2.021 | 0.989 | 2.072 | 1.003 | |
1KGP CHS (100) | NA | NA | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 2.110 | 1.118 | |
Stop-gained† | 1KJPN (1,070) high-confidence | 0.005 | 0.081 | 0.004 | 0.061 | 0.753 | 0.747 | 11.303 | 2.713 | 12.064 | 2.813 |
1KJPN (1,070) high-sensitive | 0.008 | 0.101 | 0.008 | 0.101 | 0.099 | 0.302 | 12.101 | 2.853 | 12.217 | 2.851 | |
1KGP JPT (89) | NA | NA | NA | NA | 0.067 | 0.252 | 11.315 | 2.898 | 11.382 | 2.914 | |
1KGP CHB (97) | NA | NA | NA | NA | 0.052 | 0.222 | 12.093 | 2.758 | 12.144 | 2.769 | |
1KGP CHS (100) | NA | NA | 0.000 | 0.000 | 0.070 | 0.326 | 12.900 | 3.047 | 12.970 | 3.096 |