This report provides an assessment of coverage for $name.
It contains the following sections:
Summary including per gene coverage chart.
Table of exons with sub-optimal coverage (<100% coverage at $threshold).
Interactive plots of exons with sub-optimal coverage.
A summary table of average coverage across all genes.
Full gene coverage plots.
Table of per exon coverage across all genes.
Coverage of known variants (if specified).
n.b. all coverage plots are displayed relative to the + strand.
Summary
$build
$panel
Genes in the applied panel(s): $total_genes
Total selected transcripts: $total_transcripts
Low coverage threshold: < $threshold
Panel coverage at $threshold: $panel_pct_coverage %
Genes with 100% coverage at $threshold: $fully_covered_genes
Genes not 100% covered at $threshold: $gene_issues
$summary_text
$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.
Plot
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
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