Coverage Summary

If a panel is selected, the app calculates the coverage information based on the on-target genes.

Coverage Uniformity Information Table
Statistic	Definition
Median CV	The median coefficient of variation of coverage of the 1000 most highly expressed transcripts, as reported by the CollectRnaSeqMetrics utility from Picard tools. Ideal value = 0.
Median 3′	The median uniformity of coverage of the 1000 most highly expressed transcripts at the 3′ end, as reported by the CollectRnaSeqMetrics utility from Picard tools. 3′ bias is calculated per transcript as the mean coverage of the 3′ most 100 bases divided by the mean coverage of the whole transcript.
Median 5′	The median uniformity of coverage of the 1000 most highly expressed transcripts at the 5′ end, as reported by the CollectRnaSeqMetrics utility from Picard tools. 5′ bias is calculated per transcript as the mean coverage of the 5′ most 100 bases divided by the mean coverage of the whole transcript.
Reads aligned to correct strand	Percentage of reads that align to the expected strand of annotated transcripts, as reported by the CollectRnaSeqMetrics utility from Picard tools.

If a panel is selected, the app calculates the alignment information based on the on-target genes.

Alignment Information Table
Statistic	Description
Coding	Metrics based on coding bases.
UTR	Metrics based on bases in untranslated regions (UTR).
Intron	Metrics based on bases in introns.
Non-targeted	Metrics based on bases in intergenic or non-targeted regions. The app reports "non-targeted" if a panel is selected.
Fold Coverage	The total number of bases in the category divided by the size of the entire category.
% Bases	The total number of bases aligned to this region relative to the total number of aligned bases.

If a panel is selected, the app calculates the gene-level coverage information based on the on-target genes.

Gene-Level Coverage Table
Coverage	Number of Genes
1X	Number of genes covered at the mean base coverage level or deeper.
10X
30X
100X