View coverage metrics

You can view the following information in the View Coverage Metrics tab of the Variant Calls by Allele table. The columns that are available on this tab vary according to the run type.

Column	Description
Total Read Cov	Total read coverage at this position, after downsampling. Variants calls are made on a sample of reads when coverage is higher than specified in the parameter settings file. This is referred to as "downsampling". For more information, see downsample_to_coverage in variantCaller plugin advanced parameters.
Read Cov +	Total read coverage on the forward strand, after downsampling.
Read Cov -	Total read coverage on the reverse strand, after downsampling.
Allele Read Cov	The number of reads that contain this allele, after downsampling.
Allele Read Freq ^[1]	The frequency of this allele across all reads.
Total Mol Cov ¹	The number of molecules covering this location.
Allele Mol Cov ¹	The number of detected molecules containing this allele.
Allele Mol Freq ¹	The frequency of molecules containing this allele.
Allele Cov + ¹	Allele coverage on the forward strand, after downsampling.
Allele Cov - ^[2]	Allele coverage on the reverse strand, after downsampling.
Strand bias	The discrepancy between allele frequencies on the forward and reverse strands.

¹ This column is unavailable for sequencing runs that use Tag Sequencing or Ion AmpliSeq™ HD as the target technique.

² This column is unavailable for sequencing runs that use Tag Sequencing as the target technique.

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