Fig. 2: Violin plots comparing scores of the selected seven variant analysis tools. | npj Genomic Medicine

Fig. 2: Violin plots comparing scores of the selected seven variant analysis tools.

From: A robust pipeline for ranking carrier frequencies of autosomal recessive and X-linked Mendelian disorders

Fig. 2

All gnomAD missense variants defined as pathogenic/likely pathogenic and benign/likely benign in ClinVar were evaluated. Violin plots illustrate the median value (dot) and the 25th to 75th percentile range (black line). In each plot, benign variants are on the left and pathogenic variants are on the right. The deleteriousness scores are along the y-axis. Higher values indicated a higher probability that the variant is damaging in all scores except for SIFT, where a low score is associated with deleteriousness. The y-axis for CADD is a logarithmically transformed score, and the rest are linear probabilities. The x-axis represents the probability density of variants along the range of scores. The CADD plot appears different because its y-axis is on a logarithmic instead of linear scale. Calculated mean scores with standard deviations are listed in Supplementary Dataset 4. See also Supplementary Fig. 1.

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