I need to find more available SNPs to narrow down my mutations which are on LGIV, and I used to find the SNPs on http://genome.wustl.edu/services/c-elegans-snpdata/?chrom=4 years ago. But when I use this website today, it can’t show the SNP information, ‘404 Error’ instead, I wonder any other SNP databases available?
Your link is now working, at least for me, though I’m sure there are much more comprehensive databases now available.
PS if you want another graphical interface that will show you more SNPs (though without the digest predictions), there’s always the Genome Browser within WormBase; if you don’t already see the SNPs, use “select tracks” and activate the “polymorphisms” track. If you do this, remember to make sure which strain the polymorphism was found in, though, it might not be CB4856.
I’m pretty sure there is a better way to get a list of CB4856 SNPs, but can’t immediately recall it.
The quickest way to get the list of Hawaiian SNPs used for mapping is from CloudMap’s shared data library on Galaxy (https://usegalaxy.org/library/list#folders/F4894f62515c7cbb9). Note that it corresponds to genome version WS220, so you’ll need to use the same reference for alignment.
If you need a more recent version (WS235 or later), I have one that I parsed from the Variation field of WormBase. PM me and I’ll send it.
Harold