rice SNPs annotation
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Frans Maathuis
Dec 13, 2016, 10:50:11 AM12/13/16
to gen...@soe.ucsc.edu
hello
i have query about your rice genome browser: as far as i can make out, your annotations are either based on MSUv6 (and shifted by ~0.5kb compared to MSUv7, see below for example locus 06g48800 coordinates) and you mapped SNPs on your v6 framework using the 44/700k genechip from the McCouch lab (Cornell) and used their SNP coordinates (which are based on MSU v7). this means positioning of SNPs would be completely wrong (for example SNP chr08:29 535 341 which should be at the beginning of exon 2 of Os06g48800, is in the middle of exon 1 in your annotation!) and SNP effects (e.g. amino acid substitutions) do not make any sense. i haven't exhaustively checked, but assume all your SNP positions are incorrect. things get even more (worryingly) weird when v7 is used in your browser; the SNP is still in the wrong place but its identifier does no longer bear any relation to the scale on top of your browser.
regards
frans maathuis
i have query about your rice genome browser: as far as i can make out, your annotations are either based on MSUv6 (and shifted by ~0.5kb compared to MSUv7, see below for example locus 06g48800 coordinates) and you mapped SNPs on your v6 framework using the 44/700k genechip from the McCouch lab (Cornell) and used their SNP coordinates (which are based on MSU v7). this means positioning of SNPs would be completely wrong (for example SNP chr08:29 535 341 which should be at the beginning of exon 2 of Os06g48800, is in the middle of exon 1 in your annotation!) and SNP effects (e.g. amino acid substitutions) do not make any sense. i haven't exhaustively checked, but assume all your SNP positions are incorrect. things get even more (worryingly) weird when v7 is used in your browser; the SNP is still in the wrong place but its identifier does no longer bear any relation to the scale on top of your browser.
regards
frans maathuis
UCSC/MSUv6:
LOC_Os06g48800.1
Score: 946
Position: chr6:29533807-29535555
IRC (IRRI):
LOC_Os06g48800
Type
gene
Description
OsHKT2;4 - Na+
transporter, expressed
Position
chr06:29534805..29536553
(- strand)
Phytozome
| Defline: | OsHKT2;4 - Na+ transporter, expressed |
| Organism Name: | O. sativa |
| Length: | 1749 |
| Chromosome Location: | Chr6: 29534805-29536553 |
-- Frans Maathuis Biology Department University of York York YO10 5DD United Kingdom Tel 44 (0)1904 328652
Luvina Guruvadoo
Dec 15, 2016, 5:55:19 PM12/15/16
to Frans Maathuis, gen...@soe.ucsc.edu
Hello Frans,
Thank you for your question. It appears you are using a mirror site and not our main site at http://genome.ucsc.edu.
We suggest you contact the folks who are hosting the rice genome browser: https://ricediversity.org/
If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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