Changes

From Genome Analysis Wiki
Jump to: navigation, search

VcfCodingSnps

1 byte removed, 13:59, 13 December 2009
no edit summary
1. A detailed instruction on using the table browser could be found at [http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help genome.ucsc.edu/cgi-bin/hgTables].
2. One can specify the regieon region to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570).
Here is an example of input gene file headlines:
5'UTR=A26C2[-] means the SNP is in the 5'UTR region of gene A26C2 with a minus strand.
INTRONIC=POTEG[-] means the SNP is in the intronic region of gene POTEG with a minus strand.
SYNONYMOUS_CODING=GAB4:Ala15826157Ala[-] means that the SNP is synonymous coding at position 15826157 in gene GAB4 with a minus strand and it keeps amino-acid Ala unchagedunchanged.
NON_SYNONYMOUS_CODING=GAB4:Leu15830952Pro[-] means that the SNP is non_synonymous coding at position 15830925 in gene GAB4 with a minus strand and it changes amino-acid Leu to Pro.
SPLICE_SITE=NCAPH2[+] means that the SNP is in the SPLICE_SITE (5 bp within exon start or end positions in the coding reegionregion) of gene MCAPH2 with a plus strand.
STOP_GAINED=MAPK12:Trp49035685stop[-] means that the SNP is at position 49035685 in gene MAPK12 with a minus strand and it changes amino-acid Trp to a stop codon.
76
edits

Navigation menu