Table 1

Predicted functional consequence of SNPs and indels

Consequence

SNPs

Indels


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


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.

Wong et al. Genome Biology 2012 13:R72   doi:10.1186/gb-2012-13-8-r72

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