appendix_b
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— | appendix_b [2012/02/13 11:31] (current) – created - external edit 127.0.0.1 | ||
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+ | ====== MapSNPs annotation summary report explained ====== | ||
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+ | 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/ | ||
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+ | Columns 18-32 will contain "?" | ||
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+ | __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 '' | ||
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+ | ^ Column\\ No. ^ Column\\ Name ^ Description | ||
+ | | 1 | snp_pos | ||
+ | | 2 | str | transcript strand (" | ||
+ | | 3 | gene | gene symbol | | ||
+ | | 4 | transcript | ||
+ | | 5 | ccid | UCSC canonical cluster ID (number) | | ||
+ | | 6 | ccds | NCBI CCDS cluster ID | | ||
+ | | 7 | cciden | ||
+ | | 8 | refa | reference allele / variant allele (" | ||
+ | | 9 | type | SNP functional category (" | ||
+ | | 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 | ||
+ | | 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 (" | ||
+ | | 17 | jxacc | distance from mutation position to the nearest acceptor intron / exon junction (" | ||
+ | | 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) " | ||
+ | | 22 | cdnpos | ||
+ | | 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 | ||
+ | | 32 | refs_acc | ||
+ | | 33 | dbrsid | ||
+ | | 34 | dbobsrvd | ||
+ | | 35 | dbavHet | ||
+ | | 36 | dbavHetSE | dbSNP standard error for the average heterozygosity | | ||
+ | | 37 | dbRmPaPt | ||
+ | | 38 | Comments | ||
appendix_b.txt · Last modified: 2012/02/13 11:31 by 127.0.0.1