Genes coverage section

The Genes coverage section helps you quickly identify parts of genes that may not have been adequately sequenced in your case. This insight is particularly important when assessing sequencing quality, interpreting uncertain findings, or deciding if further validation is needed.

While variant callers provide base-by-base coverage, Emedgene simplifies the view by showing average coverage per region. This makes it easier for you to spot undercovered genes at a glance, even when individual positions may appear sufficiently covered. By smoothing out local fluctuations, average coverage helps you prioritize regions that might require further review and complements DRAGEN's fine-grained metrics with a broader, more interpretable view.

How coverage is calculated

Coverage metrics are generated differently depending on the type of input data used for your case:

1. FASTQ / BAM or gVCF-based cases

• If your case was started from FastQ/BAM or gVCF, coverage is inferred from gVCF reference blocks (also called GVCFBlocks).

• These blocks are segments of the genome where genotype quality (GQ) is consistent.

• A new block is created whenever there's a significant change in GQ, which results in a highly segmented and detailed representation of local sequencing quality.

• Coverage for a region is based on the median coverage of each gVCF block. If a region spans multiple blocks, the reported value is the average of those medians.

• Within a region (like an exon), you’ll often see multiple blocks. Emedgene aggregates them to show you:

  • Average depth

  • Minimum depth

  • Depth range

• Occasionally, some blocks may be unusually large and may miss internal variation—for example, in genes like XIAP, one block could span an entire region despite having uneven coverage inside.

2. VCF + BAM or VCF + BED-based Cases

• If your case includes VCF and BAM or VCF and BED, coverage is calculated directly from the aligned reads or from predefined BED intervals.

• Coverage is calculated as the true base-by-base average across the entire region.

• This method avoids the variability of gVCF segmentation and gives a precise coverage profile for each region.

Regions evaluated for coverage

Coverage is compared against expected regions defined in:

• Emedgene's reference BED file, or

• Your test’s custom KIT BED file

Each region is defined by:

• Chromosome

• Start & end positions

• Name and strand (Optional)

Coverage assessment

Emedgene uses the tool bedtools intersect to compare each expected region from the regions used for coverage assessment against actual read coverage. The system captures:

• How much of the region overlaps with sequenced data

• Depth of coverage per segment

Coverage statistics

Each region includes these metrics:

How to use the coverage tool

You can interactively explore gene-level coverage details using the Genes with Insufficient Coverage tab. This tool is currently available only for FASTQ-based cases.

Here’s what you can do:

• Search for a specific gene or a list of genes.

• Filter results based on coverage thresholds:

  • ≤0x

  • ≤5x

  • ≤10x

  • ≤20x

  • or All

• Download tables or genomic coordinates for regions with poor coverage.

• Click More details to open a pop-up with exact genomic coordinates of low-coverage blocks.

To check coverage for a gene:

1. Enter the gene symbol in the search box and select it.

2. Choose your desired coverage filter from the dropdown.

3. Review the results in the table or download the data.

4. Click More details to inspect the specific coordinates of undercovered regions.

To look up the coverage for multiple genes that are saved as a Gene list:

Click the Add Gene List button and select any of your pre-loaded gene lists.

To further filter regions:

• By maximum depth of coverage

  Select Coverage, then choose the highest allowable coverage value from the dropdown list,

• By percentage of bases covered >20×

  Select % of Bases Gt20, then choose the highest allowable percentage from the dropdown list.

Visual review in IGV allows manual variant confirmation by inspecting aligned reads at specific genomic regions.

To inspect poorly covered regions of a gene in the desktop IGV browser:

1. Click on More details in the row corresponding to the gene of interest. This opens a pop-up with coverage details for the selected gene.

2. In the pop-up, select View on IGV to open the region in the IGV desktop application.

To download data

Click the Download button to export the full list of low-coverage regions as a *_insufficient_regions.tsv file. Each row includes region coordinates and all metrics.

Each row corresponds to one region and includes:

• Region coordinates

• Calculated coverage metrics

• Region length

Use this file to:

• Compare multiple cases

• Track sequencing gaps

• Plan confirmatory testing

• Share results with collaborators