Table 2.
Per individual variant load at conserved sites
| Variant type | Number of derived variant sites per individual |
Excess rare deleterious |
Excess low- frequency deleterious |
||
|---|---|---|---|---|---|
| Derived allele frequency across sample | |||||
| <0.5% | 0.5%-5% | >l5% | |||
| All sites | 30K-150K | 120K- 680K |
3.6M- 3.9M |
- | - |
| Synonymous a | 29-120 | 82-420 | 1.3K-1.4K | - | - |
| Nonsynonymous a | 130-400 | 240-910 | 2.3K-2.7K | 76-190b | 77-130b |
| Stop-gain a | 3.9-10 | 5.3-19 | 24-28 | 3.4-7.5b | 3.8-11b |
| Stop-loss | 1.0-1.2 | 1.0-1.9 | 2.1-2.8 | 0.81-1.1b | 0.80-1.0b |
| HGMD-DM a | 2.5-5.1 | 4.8-17 | 11-18 | 1.6-4.7b | 3.8-12b |
| COSMIC a | 1.3-2.0 | 1.8-5.1 | 5.2-10 | 0.93-1.6b | 1.3-2.0b |
| Indel-frameshift | 1.0-1.3 | 11-24 | 60-66 | -d | 3.2-11b |
| Indel-non-frameshift | 2.1-2.3 | 9.5-24 | 67-71 | -d | 0-0.73b |
| Splice site donor | 1.7-3.6 | 2.4-7.2 | 2.6-5.2 | 1.6-3.3b | 3.1-6.2b |
| Splice site acceptor | 1.5-2.9 | 1.5-4.0 | 2.1-4.6 | 1.4-2.6b | 1.2-3.3b |
| UTR a | 120-430 | 300-1.4K | 3.5K-4.0K | 0-350c | 0-1.2Kc |
| Non-coding RNA a | 3.9-17 | 14-70 | 180 -200 | 0.62-2.6c | 3.4-13c |
|
Motif gain in TF
peak a |
4.7-14 | 23-59 | 170-180 | 0-2.6c | 3.8-15c |
|
Motif loss in TF
peak a |
18-69 | 71-300 | 580-650 | 7.7-22c | 37-110c |
| Other conserved a | 2.0K-9.9K | 7.1K-39K | 120K-130K | - | |
| Total conserved | 2.3K-11K | 7.7K-42K | 130K-150K | 150-510 | 250-1.3K |
Only sites where ancestral state can be assigned with high confidence reported.
Ranges reported are across populations.
a
Sites with GERP>2
b
Using Synonymous sites as base-line
c
Using ‘Other conserved’ as base-line
d
Rare indels were filtered in Phase 1