SNPEff output meaning
Hi everyone,
I wonder if anyone can help understand this SNPEff output:
chr pos strain gene_name type effect_impact ref alt codon_change amino_acid_change
1 20136579 6911 RAP2.12 frameshift_variant+stop_lost HIGH TG T tga/ p.Ter357fs/c.1070delG
What I'd like to understand is what the 'amino_acid_change' means with: p.Ter357fs/c.1070delG
Sorry if the question doesn't sound clear, but I'm new here.
Thanks for your help
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simone.castellana •
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simone.castellana •
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It is actually TGA, which is the stop codon, and G is deleted so it says deletion of G on Ter(minating) sequence.
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This is a more genetic question than a bioinformatic related question. Anyway I do recommend checking the website for Sequence Variant Nomenclature available here: https://varnomen.hgvs.org/. There, under DNA section check for deletion : https://varnomen.hgvs.org/recommendations/DNA/variant/deletion/