From Genome Analysis Wiki
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Some possible annotating results for a single SNP with the meanings of their output format are listed below:
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 unchanged. 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 region) 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.
The annotating result will be added to the entry "INFO" of the input VCF SNP file and outputted together with other information. Here is an example of output VCF file headlines: