Coverage

In this notebook, we calculate coverage across the whole-genome and specifically at the SNP targets of the amplicon panel. Coverage refers to the number of sequencing reads that align to a specific region of the genome. Higher coverage provides greater confidence in variant calls and helps detect low-frequency alleles.

Whole-genome

Lets plot coverage across the whole genome to see if we have off-target coverage! Off-target reads occur when primers amplify unintended regions of the genome, resulting in coverage at locations outside the targeted amplicons.

Coverage at each target SNP

Target SNP coverage is a critical quality metric that indicates how well each intended mutation site was amplified. Sufficient coverage is essential for accurate genotyping and allele frequency estimation.

Coverage by sample

Coverage by amplicon and sample

Amplicon by sample read depth (.xlsx)