Fig 1.
(a) This illustration shows the concept of two SNVs affecting the same codon resulting in different prediction outcomes. (b) Second site variants within the same codon turn premature stop codons predicted by SnpEff into amino acid substitutions. In 144 cases, premature stop codons are substitutions by the respective amino acids. (c) The proportion of amino acid changing variants is significantly higher in genes with premature stop codons predicted by NAVIP (blue) compared to all other genes (red). aaN is the number of variants changing an amino acid residue and aaS is the number of variants resulting in the same amino acid residue. (d) The proportion of amino acid changing variants is significantly higher in genes with premature stop codons predicted by SnpEff (blue) compared to all other genes (red). Data underlying these visualizations are available in S3 File. (e) Comparison of the average expression of genes with a premature stop codon predicted by NAVIP against all other protein encoding genes with available expression data. (f) Comparison of the average expression of genes with a premature stop codon predicted by SnpEff against all other protein encoding genes with available expression data.
Fig 2.
(a) Theoretical concept of two InDels compensating each others’ frameshift. The first insertion changes the reading frame, while the second insertion shifts the reading frame back to the original one. While each individual variant would suggest a loss-of-function due to a frameshift mutation, the combination of both results in ‘only’ two additional amino acids in the gene product. (b) Distribution of distances between compensating InDels (cInDels). As the second InDel can compensate for the frameshift caused by the upstream InDel, distances between such cInDels are short and frequently multiples of three. In total, 484 genes were identified to contain cInDels in the Nd-1 data set.