Table 1 |
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Predicted functional consequence of SNPs and indels |
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|
Consequence |
SNPs |
Indels |
|
|
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|
5 kb upstream or downstream |
345,321 |
86,229 |
|
5' or 3' UTR |
19,402 |
3,769 |
|
Intronic |
864,790 |
173,237 |
|
Synonymous coding |
13,697 |
NA |
|
Non-synonymous coding |
7,880 |
NA |
|
Essential splice site |
10a (19) |
0a (3) |
|
Stop gain |
42a (71) |
NA |
|
Stop lost |
6a (16) |
NA |
|
In-frame codon insertion or deletion |
NA |
140 |
|
Frameshift |
NA |
126 |
|
Two or more consequences |
689,535 |
136,895 |
|
Within non-coding gene or mature microRNA |
115,453 |
22,735 |
|
5 kb upstream or downstream of non-coding gene |
163,280 |
31,988 |
|
Intergenic (>5 kb from a coding or non-coding gene) |
2,247,487 |
416,289 |
|
|
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A SNP or indel is annotated with a single consequence if the SNP or indel has the same effect on all protein-coding transcripts of a gene. A SNP or indel has two or more consequences if it has different effects on different transcripts of a gene. For example, a SNP may be in the intron of one transcript, and a synonymous SNP in a second transcript. Consequences were predicted using the Ensembl Variant Effect Predictor (VEP) [23] and gene models from Ensembl version 64. Note that a SNP may belong to more than one category. For example, a SNP may be a synonymous SNP in one gene and also within 5 kb of a second gene. aThe number of true stop codon gain, stop loss, and essential splice site consequences after manual inspection. The number in parentheses is the predicted number from VEP (Tables s1, s2 and s3 in Additional file 1). NA, not applicable. |
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Wong et al. Genome Biology 2012 13:R72 doi:10.1186/gb-2012-13-8-r72 |
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