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



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.