Figure 3: Coverage Analysis. | Scientific Reports

Figure 3: Coverage Analysis.

From: A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape

Figure 3

Analysis of the depth of coverage of the samples in the validation set. (a) The percentage of bases of the ROIs above a given coverage level. The red vertical line corresponds to C30 (98.4%). (b) The relationship between GC content and depth of coverage. Each dot represents a single exon. GC content was computed as the percentage of G/C in the exon sequence. The coverage was computed as the mean coverage of the exon over all samples in the validation set. (c) Density plot showing the coverage distribution along all ROIs over all samples in the validation set. The exon is represented as a black box and intron/exon boundaries as grey lines. The exonic coverage was computed as the mean over 200 equally sized windows to normalize the exon length. Intronic coverage is plotted as one position per base. The blue background represents the density of exons with a given coverage at a given position. The yellow line represents the mean coverage, the dashed orange lines represent the Q1 and Q3 quartiles and the dotted orange lines the 5 and 95 percentiles. Finally, the purple horizontal line represents the mean coverage and the red line the minimum coverage threshold of 30x.

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