Hi all, I'm currently working with forward genetics mutagenesis in zebrafish, and working on finding underlying mutations. I have a question regarding annotations of SNVs.
I have few SNVs annotated as Stop Codon but are also mentioned in dbSNP as SNP, for example https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=515365675 .
Now as I have many wild type samples too, I cant find this SNPs in homozygous or heterozygous state. So, I want to know if I should keep these SNPs or discard. Also, Zebrafish has dbSNP build 142 latest but aligned to later genome assembly zv9, but enembl says they are now mapped to GRCz10 (http://www.ensembl.org/info/genome/variation/sources_documentation.html#danio_rerio) . I guess all SNPs in dbSNPs are mapped to GRCz10.
