A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w 1118 ; iso-2; iso-3
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We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants in genome sequences. Once a genome is sequenced, SnpEff annotates variants based on their genomic locations and predicts coding effects. Annotated genomic locations include intronic, untranslated region, upstream, downstream, splice site, or intergenic regions. Coding effects such as synonymous or non-synonymous amino acid replacement, start codon gains or losses, stop codon gains or losses, or frame shifts can be predicted. Here the use of SnpEff is illustrated by annotating ~356,660 candidate SNPs in ~117 Mb unique sequences, representing a substitution rate of ~1/305 nucleotides, between the Drosophila melanogaster w(1118); iso-2; iso-3 strain and the reference y(1); cn(1) bw(1) sp(1) strain. We show that ~15,842 SNPs are synonymous and ~4,467 SNPs are non-synonymous (N/S ~0.28). The remaining SNPs are in other categories, such as stop codon gains (38 SNPs), stop codon losses (8 SNPs), and start codon gains (297 SNPs) in the 5'UTR. We found, as expected, that the SNP frequency is proportional to the recombination frequency (i.e., highest in the middle of chromosome arms). We also found that start-gain or stop-lost SNPs in Drosophila melanogaster often result in additions of N-terminal or C-terminal amino acids that are conserved in other Drosophila species. It appears that the 5' and 3' UTRs are reservoirs for genetic variations that changes the termini of proteins during evolution of the Drosophila genus. As genome sequencing is becoming inexpensive and routine, SnpEff enables rapid analyses of whole-genome sequencing data to be performed by an individual laboratory.
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Annotation of all 4303 unique credible NIMs using SnpEff identified 26 NIMs with high or moderate impact on genes.
“We annotated all 4303 unique credible NIMs using SnpEff (Cingolani et al., 2012) to identify a total of 26 NIMs with high (e.g., start codon loss, stop codon gain) or moderate impact (nonsynonymous variants) on genes (Figure 6b).”
From The lingering effects of Neanderthal introgression on human complex traits (2023) · cites this paper as Cingolani et al., 2012
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- Authors
- Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., & Ruden, D. M.
- Affiliations
- Wayne State University (US)
- McGill University (CA)
- Corresponding author
- Ruden, Douglas M.
- Venue
- Fly
- Publisher
- Informa UK Limited
- Published
- 2012-04
- Volume
- 6
- Issue
- 2
- Pages
- 80-92
- ISSN
- 1933-6934 (ISSN-L)
- 1933-6942
- PMC
- PMC3679285
- OpenAlex
- W2106578986
- Cited by
- 11,816
- References
- 44
- Citations by year
- 2026: 1068 · 2025: 1370 · 2024: 1488 · 2023: 1187 · 2022: 1300 · 2021: 1231 · 2020: 1032 · 2019: 783 · 2018: 634 · 2017: 570 · 2016: 464 · 2015: 324 · 2014: 240 · 2013: 103 · 2012: 13
- FWCI
- 87.36
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- other-oa
- Locations
- Fly (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Wayne State University (ES012933)
- Broad Institute
- National Institutes of Health (5p30es006639-15, NIH-R01, ES06639, P30 ES06639)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK071073)
- National Institute of Environmental Health Sciences (P-30-ES06639, P30-ES006639, R01ES012933, R21ES021983)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- SnpEff, single nucleotide polymorphisms, variant annotation, 5' untranslated region, 3' untranslated region, splice sites, recombination frequency, Drosophila melanogaster
- MeSH terms
- Animals, Drosophila melanogaster, Male, Software, Polymorphism, Single Nucleotide, Genome, Insect, Molecular Sequence Annotation
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