Analysis Output | Analysis Reports | Summary Analysis Report

Summary Analysis Report

The RNA-Seq Alignment App provides an aggregate summary for all the samples.

Table 6 Summary Table
Statistic	Definition
Sample ID	The sample ID.
Read Length	The length of reads.
Number of Reads	The total number of reads passing filter for this sample.
% Total Aligned	Percentage of reads passing filter that aligned to the reference, including abundant reads.
% Abundant	Percentage of reads that align to abundant transcripts, such as mitochondrial and ribosomal sequences.
% Unaligned	Percentage of reads that do not align to the reference.
Median CV Coverage Uniformity	The median coefficient of variation of coverage of the 1000 most highly expressed transcript, as reported by the CollectRnaSeqMetrics utility from Picard tools. Ideal value = 0.
% Stranded	Percentage of reads that are stranded.