snpEff

SnpEff is an efficient computer program designed to categorize variants' effects in genome sequences. It annotates variants based on their genomic locations and predicts coding effects. One of the key features of SnpEff is that it provides annotated genomic locations such as intronic, untranslated regions, upstream, downstream, splice site, or intergenic regions. Moreover, it predicts coding effects such as synonymous or non-synonymous amino acid replacement, start codon gains or losses, stop codon gains or losses, or frameshifts.

SnpEff has been widely used in many studies, and its efficacy has been demonstrated in various research areas. For instance, it has been applied to annotate approximately 356,660 candidate SNPs in about 117 Mb unique sequences, representing a substitution rate of approximately 1/305 nucleotides between two Drosophila melanogaster strains. In this study, SnpEff showed that approximately 15,842 SNPs are synonymous, and around 4,467 SNPs are non-synonymous, with an N/S ratio of about 0.28. The remaining SNPs were categorized into other categories, such as stop codon gains (38 SNPs), stop codon losses (8 SNPs), and start codon gains (297 SNPs) in the 5'UTR.

Another interesting finding from the study was that SnpEff showed that the SNP frequency is proportional to the recombination frequency, i.e., highest in the middle of chromosome arms. Additionally, it 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. The 5' and 3' UTRs appear as reservoirs for genetic variations that change the termini of proteins during the evolution of the Drosophila genus.