Coverage report for sample: $name


Report details

This report provides an assessment of coverage for $name.

It contains the following sections:

Summary

$summary_plot




Exons with <100% coverage at $threshold

Of the $total_genes genes ($total_transcripts transcripts) included in the panel, $exon_issues exons in $gene_issues genes had sub optimal-coverage.



To assess what portion of the exon(s) have sub-optimal coverage, the plots below display an interactive window on hovering, showing the coverage at that current base.
The top right also contains a toolbar, with functions such as panning and zooming.






Per gene coverage summary


The following section provides coverage metrics of each gene.
The table below contains metrics for each gene averaged across all of its exons. Plots of each gene are also included below.

$gene_table_headings







Per exon coverage


The following section provides coverage metrics for every exon of each gene.

$exon_table_headings



Coverage of Known Variants


Below are tables giving coverage of known variants. The low coverage table gives those not covered at $threshold, and the high coverage table contains those covered above $threshold.

  • $total_snps variants were within the given panel regions and included for analysis
  • $snps_covered ($snps_pct_covered %) were covered at or above $threshold
  • $snps_not_covered ($snps_pct_not_covered %) variants were not covered at $threshold
  • $snps_out_panel ($snps_pct_out_panel %) variants spanned region boundaries
  • $vcfs


  • Variants spanning gene / exon boundaries (e.g. larger structural variants)
    VCF Chromosome Position Ref Alt Info



    Table of variants with low coverage (< $threshold)
    VCF Gene Exon Chromosome Position Ref Alt Coverage



    Table of variants with high coverage (>= $threshold)  
    VCF Gene Exon Chromosome Position Ref Alt Coverage


    Coverage per chromosome



    The following section provides an overview of global read coverage per chromosome. Please note that if the source data is derived from a target-capture assay, coverage data will be plotted within target regions only.

    $coverage_per_chromosome_fig