viewing hgvs in genome data viewer
So I am using this ncbi viewer to visualize NM_000106.5:c.775delA within NM_000106.5. This is extremely handy and I can see the variant at the coding DNA reference sequence. But is there any way within this view to zoom out and see where this location is in the linear genomic reference sequence GCF_000001405.40?
I tried searching ncbi viewer for NM_000106.5:c.775delA within GCF_000001405.40 and it does give me a position but it seems to be relative to NM_000106.6.
I want to ensure that I know the corresponding genomic position for M_000106.5:c.775delA with certainty (or is my second search the answer)?
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You may want to use NCBI Genome Data viewer instead: https://www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCF_000001405.40
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NM_000106.5:c.775delAin search assembly to get this view.That is what I was doing originally, but if you look in your picture under "transcript" (blue bar) it says NM_000106.6 not NM_000106.5. I am concerned there might be small differences between the sequences/positions
You are always going to find the latest revision of a sequence in these viewers. You can check on the revision history to see what difference there may be between the versions by checking: https://www.ncbi.nlm.nih.gov/nuccore/NM_000106/?report=girevhist
More detail: https://www.ncbi.nlm.nih.gov/sviewer/girevhist-diff/girevhist-diff.cgi?tool=portal&db=nuccore&frst=1435110251_46_165194071_Jul%2027,%202018%2012:55%20PM_6_1&scnd=392513720_46_161804281_Jul%208,%202018%2011:23%20AM_5_1&history_fmt=fasta
It looks like there was a substantial change in the sequence between the two versions.
Thanks so much!