General cohort-level characteristics of alignments and variant calls with T2T-CHM13 in comparison with previous assemblies
| T2T-CHM13 | GRCh37 | GRCh38 | |
|---|---|---|---|
| Ungapped length (bp) | 3,117,275,501 | 2,861,327,195 | 2,937,639,396 |
| Avg. % coverage (min/max) | 39.0 (20.3/105.9) | 39.8 (21.3/107.7) | 40.2 (21.5/108.7) |
| Number of variant sitesa | 47,744,487 | 35,571,130 | 37,938,450 |
| Variant rate (variants/kbp)a,b | 15.3 | 12.4 | 12.9 |
| Number of SNV sites (not in dbSNPv155) | 41,931,920 (10,806,250) | 30,866,176 (14,806,371) | 33,133,695 (12,070,889) |
| Number of indel sites (not in dbSNPv155) | 6,650,809 (3,709,821) | 5,089,447 (3,170,927) | 5,221,969 (2,457,457) |
| Ts/Tv ratio | 1.50 | 1.95 | 1.80 |
| Number of common variants (MAF ≥ 5%)c | 9,468,024 | 9,800,121 | 9,832,496 |
| Number of low-frequency variants (MAF < 5%)c | 43,151,191 | 29,714,010 | 31,895,019 |
| Number of rare variants (MAF < 1%)c | 37,402,076 | 24,807,638 | 26,741,004 |
| Number of singletons (per kbp) [% of total variants] | 19,077,986 (6.12) [40.0] | 11,502,698 (4.02) [32.3] | 13,547,273 (4.61) [35.7] |
| Number of nonreference alleles with AF > 50% | 1,940,331 | 2,424,122 | 2,465,936 |
| Number of LoF variants (% of total variants) [in ClinVar genes] | 17,446 (0.037) [17,297] | 12,628 (0.036) [12,326] | 12,829 (0.034) [12,517] |
| Number of variants with low/medium/high impact (% of total variants) | 168,420/208,625/22,848 (0.353/0.437/0.048) | 153,001/184,694/16,392 (0.426/0.514/0.045) | 155,088/188,347/16,542 (0.409/0.496/0.044) |
[i] (Ts) transition, (Tv) transversion, (MAF) minor allele frequency, (AF) allele frequency, (LoF) loss of function.
[ii] aMultiallelic variants were only counted once.
[iii] bBased on ungapped length.
[iv] cEach alternative allele was counted separately. If an alternative allele had a frequency >50%, the reference allele was considered the minor allele.