Table 1.
Summary of differential breakpoints in the merged callset
| Insertions | Deletions | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Reference | Repeat | No. of variants | Diff | Diff % | Med bp | No. of variants | Diff | Diff % | Med bp |
| GRCh38 | |||||||||
| No TR/SD | 14,961 | 882 | 5.9% | 2.2 | 5804 | 180 | 3.1% | 4.9 | |
| SD no TR | 2609 | 440 | 16.9% | 3.5 | 1922 | 402 | 20.9% | 5.0 | |
| All | 60,716 | 19,589 | 32.3% | 19.4 | 38,442 | 10,641 | 27.7% | 22.0 | |
| T2T-CHM13 | |||||||||
| No TR/SD | 15,180 | 888 | 5.8% | 3.4 | 11,191 | 411 | 3.7% | 3.7 | |
| SD no TR | 1752 | 419 | 23.9% | 4.5 | 2014 | 506 | 25.1% | 14.0 | |
| All | 46,862 | 12,833 | 27.4% | 19.9 | 40,420 | 11,625 | 28.8% | 24.6 | |
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Breakpoint differences increase in both GRCh38 and T2T-CHM13v2.0. (No TR/SD) SV is not anchored in TRs or SDs, (SD no TR) SV is anchored in SDs but not TRs, (All) all variants including those TRs and SDs, (Diff) number of variants with different offsets in at least one haplotype, (Diff %) mean percentage of variants with different offsets in at least one haplotype, and (Med bp) median number of bases variants with different locations are shifted.
