Table 3.
Overall characteristics of variant calls in previously unresolved regions
| Regions unresolved in | All of | ||
|---|---|---|---|
| GRCh37 | GRCh38 | T2T-CHM13 | |
| Total length (bp) | 268,965,814 | 251,330,203 | 3,117,275,501 |
| Number of variant sitesa | 8,321,170 | 7,826,115 | 47,744,487 |
| Variant rate (variants/kbp)a | 30.9 | 31.1 | 15.3 |
| Number of SNV sites | 7,710,249 | 7,265,225 | 41,931,920 |
| Number of indel sites | 829,457 | 771,429 | 6,650,809 |
| Number of common variants (MAF ≥ 5%)b | 695,892 | 621,512 | 9,293,456 |
| Number of low-frequency variants (MAF < 5%)b | 8,670,575 | 8,211,562 | 43,103,217 |
| Number of rare variants (MAF < 1%)b | 7,721,885 | 7,316,843 | 37,800,790 |
| Number of singletons (% of total variants) | 2,540,127 (30.5) | 2,335,181 (29.8) | 19,077,986 (40.0) |
| Number of LoF variants | 185 | 99 | 17,446 |
| Number of variants with low/medium/high impact (% of total variants) | 1,435/2,102/286 (0.017/0.025/0.003) |
719/1,048/155 (0.009/0.013/0.002) |
168,420/208,625/22,848 (0.353/0.437/0.048) |
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(MAF) minor allele frequency, (LoF) loss of function.
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aMultiallelic variants were only counted once.
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bEach alternative allele was counted separately. If an alternative allele had a frequency >50%, the reference allele was considered the minor allele.
