MapSNPs annotation summary report explained

Following is a description of MapSNPs annotation summary report. MapSNPs genomic SNP annotation tool is part of the PolyPhen-2 Batch query web service. Whenever you submit genomic SNPs in the form of chromosome coordinates/alleles, a report formatted as described below will appear under SNPs link on the Batch query results web page. It is a plain text tab-separated file with each line annotating a corresponding protein sequence variant (amino acid residue substitution) for each missense allelic variant found in input.

Columns 18-32 will contain “?” placeholders for SNPs annotated as non-coding; columns 33-37 will have values only for SNPs annotated in dbSNP build 132.

Note: MapSNPs as a part of PolyPhen-2 Batch query service, filters SNP annotations in the output depending on the user selection of SNP functional categories via Annotations menu under Advanced Options section of the input form. Selecting All disables filtering and results in annotations for all SNP categories reported in pph2-snps.txt file. However, PolyPhen-2 predictions (reported in pph2-short.txt and pph2-full.txt files) are produced for missense SNPs only, regardless of the Annotations option selected.

Column No.	Column Name	Description
1	snp_pos	input SNP chromosome:position (chromosome coordinates are 1-based)
2	str	transcript strand (“+” or “-”)
3	gene	gene symbol
4	transcript	UCSC transcript name
5	ccid	UCSC canonical cluster ID (number)
6	ccds	NCBI CCDS cluster ID
7	cciden	NCBI CCDS CDS similarity level by genomic overlap with the corresponding UCSC known gene transcript
8	refa	reference allele / variant allele (“+” strand)
9	type	SNP functional category (“coding-synon”, “intron”, “nonsense”, “missense”, “utr-3”, “utr-5”)
10	ntpos	mutation position in the full transcript nucleotide sequence (in the direction of transcription)
11	nt1	reference nucleotide (transcript strand)
12	nt2	variant nucleotide (transcript strand)
13	flanks	nucleotides flanking mutation position in the transcript sequence, enumerated in the direction of transcription (5'3')
14	trv	transversion mutation (0 - transition, 1 - transversion)
15	cpg	CpG context: 0 - non-CpG context retained, 1 - mutation removes CpG site, 2 - mutation creates new CpG site, 3 - CpG context retained: C(C/G)G
16	jxdon	distance from mutation position to the nearest donor exon / intron junction (“-” for upstream, “+” for downstream)
17	jxacc	distance from mutation position to the nearest acceptor intron / exon junction (“-” for upstream, “+” for downstream)
18	exon	mutation in exon # / of total exons (exons are enumerated in the direction of transcription)
19	cexon	same as above but for coding exons only
20	jxc	mutation in a codon that is split across two exons (? - no, 1 - yes)
21	dgn	degeneracy index for mutated codon position, by Nei & Kumar (2000) “Molecular Evolution and Phylogenetics”, page 64 (0 - non-degenerate, 2 - simple 2-fold degenerate, 3 - complex 2-fold degenerate, 4 - 4-fold degenerate)
22	cdnpos	number of the mutated codon within transcript's CDS (1-base)
23	frame	mutation position offset within the codon (0..2)
24	cdn1	reference codon nucleotides
25	cdn2	mutated codon nucleotides
26	aa1	wild type (reference) amino acid residue
27	aa2	mutant (substitution) amino acid residue
28	aapos	position of amino acid substitution in protein sequence (1-base)
29	spmap	CDS protein sequence similarity to known UniProtKB protein (? - no match)
30	spacc	UniProtKB protein accession
31	spname	UniProtKB protein entry name
32	refs_acc	RefSeq protein accession
33	dbrsid	dbSNP SNP rsID
34	dbobsrvd	dbSNP observed alleles (transcript strand)
35	dbavHet	dbSNP average heterozygosity from all observations
36	dbavHetSE	dbSNP standard error for the average heterozygosity
37	dbRmPaPt	dbSNP reference orthologous alleles in macaque (Rm), orangutan (Pa) and chimp (Pt)
38	Comments	optional user comments, copied from input