Table 1.
Description of the two 1000 Genome project non-singleton variants callsets used for running genomic coordinates conversion comparisons and description of the three chain files used for the liftover conversion.
| 1000 Genomes | low coverage | high coverage |
|---|---|---|
| Project callset | ||
| Release year | 2013 | 2020 |
| Number of samples | 2504 | 3202 |
| Variant calling | multiple callers | HaplotypeCaller |
| Aligned against | GRCh37 | GRCh38 |
| Sequencing coverage | 7.4× | 34× |
| Number of non-singleton variants | ||
| SNVs | 45 595 458 | 63 993 411 |
| Bi-allelic indels | 3 398 818 | 9 459 059 |
| Multi-allelic indels (split) | 243 179 | 4 123 095 |
| Multi-allelic indels (merged) | 108 842 | 1 375 718 |
| Non-allelic primitives | 1408 | 0 |
| Chain properties | ||
| Source assembly | GRCh37 | GRCh38 |
| Destination assembly | GRCh38 | T2T-CHM13v2.0 |
| or Clint_PTRv2 | ||
| Generation script | DoSameSpecies- | DoBlastz- |
| LiftOver.pl | ChainNet.pl | |
| Assembly aligner | BLAT | LASTZ |
| Chain file | hg19ToHg38 | hg38ToHs1 |
| (.over.chain.gz) | or hg38ToPanTro6 | |
As the high-coverage callset used exclusively the HaplotypeCaller to call variants and used longer sequencing reads, an order of magnitude more multi-allelic indels are included and non-allelic primitive variants are not present in the callset.