Coverage Analysis

Coverage of the genome or target regions for exome and targeted panel sequencing allows you to assess how comprehensively the regions of interest have been sequenced and how informative the analysis results are likely to be. This section allows you to assess both the coverage of the target regions as a whole and the coverage of individual genes and transcripts.

The "Coverage Analysis" tab is displayed only for samples uploaded in FASTQ or BAM format if the "Calculate сoverage" stage has completed successfully and gene coverage analysis is enabled.

Depth of Coverage Report

The first section contains a graph showing the proportion of the target regions covered at different depths. A table to the right of the graph shows the percentage of regions corresponding to specific coverage depths.

For example, in the graph above, 96.79% of the target regions have a coverage depth of at least 30X, which is a good indicator.

Coverage depth is expressed in units of X and indicates how many times, on average, a given position is covered by sequencing reads. For example, a coverage depth of 30X means that a given position is covered by an average of 30 reads.

Gene coverage

The second section allows you to assess the coverage of genes and transcripts of interest in greater detail. It is displayed only for samples for which saving detailed per-gene coverage is enabled.

The section contains a table of genes with the proportion of the covered region at different coverage depths: 1X, 10X, 20X, 30X, 50X, 100X, 200X, and 300X. For example, the value 30X shows what proportion of a gene or transcript is covered by at least 30 reads.

The first column contains the gene name and its Ensembl ID. Click the gene name or the icon to view coverage information for all transcripts of the gene.

The canonical transcript row is highlighted in yellow and includes either a green icon if the transcript is selected as the gene's main transcript according to MANE Select, or a black icon if the transcript is selected as the gene's main transcript according to Ensembl canonical.

The columns corresponding to different coverage depths show the percentage of the gene or transcript covered by at least the specified number of reads. For a gene, coverage information is provided for its main transcript.

The covered proportion is shown in green, and the uncovered proportion is shown in red. For example, a 61% coverage visualization looks as follows: .

To find coverage information for a specific gene or transcript, use the search by gene name, gene Ensembl ID, or transcript Ensembl ID.

Example of coverage data for the TP53 gene:

The table containing gene coverage information can be downloaded in TSV format by clicking .