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8.3 years ago
NAVANEETHAN.R
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We tried remapping the genomic coordinates of hg19 to hg38 using NCBI Remap. We got some of the locations in chromosome 1 of hg19 remapped to chromosome 9 in hg 38. Is it possible? and why it happens?
Yes getting the same result. hg19: chr1:223735638-223735888 hg38: chr9:136043353-136043603
Your fragment is localized in a segmental duplication on hg19: a long fragment of high sequence homology. However, it appears this is no longer the case in hg38. Apparently an ambigious assembly has been resolved.
So my interpretation is that in hg19 the assembler connected your piece both on chr1 and chr9. Since there are so many repetitive elements (LINEs and SINEs) there, assembly has problematic. But this was resolved in hg38 and the conclusion was that this piece is actually on chr9.
It always helps to have a look in a genome browser, and remember: the reference genome is far from perfect and is "just a reference" from a few samples with imperfect assembly. But we are gradually improving.
Maybe this fragment has a "pseudogene", that is why it remap to other location better than to wanted one.
In addition, if you use the UCSC genome browser you can add the track "hg38 diff". When using hg19 and looking at the chr1 locus, you'll see the contig is dropped from hg38. So it used to be in hg19, it's no longer in hg38.