A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

Abstract

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.

The genetic basis of parental care evolution in monogamous mice

“…Joint genotyping was subsequently performed using all gvcf files simultaneously allowing a maximum of 12 alternate alleles. We employed SnpEff version 4.3 57 to annotate and predict the effects of variants on genes.…”

Developing reduced SNP assays from whole‐genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

“…iberiensis and C‐lineage individuals using the training data set. To uncover the putative functional role of the highly differentiated SNPs, we used SNPeff 4.3 (Cingolani et al., 2012) and the NCBI honeybee annotation version 102 (Pruitt et al., 2013). Subsequently, we performed a gene ontology (GO) analysis in the DAVID v.8.0 database (Huang, Sherman, & Lempicki, 2009) considering the GO terms of the biological process (BP), molecular function (MF), cellular component (CC) (Gene Ontology Consortium, 2015) and the KEGG pathway (Kanehisa, Sato, Kawashima, Furumichi, & Tanabe, 2016).…”

Genomic analysis of the original Elberg Brucella melitensis Rev.1 vaccine strain reveals insights into virulence attenuation

“…The SNPs contained in the generated delta-encoded alignment file were fetched and reported by the show-snp utility. Next, output SNPs were converted to a VCF format using an in-house script and were subjected to annotation by the SnpEff tool [65]. The SnpEff database of the 16M genome (2002 assembly) was built based on a GenBank file that was downloaded from NCBI.…”