Statistic
Description
Uniformity of base coverage
The percentage of bases in all targeted regions (or whole genome) that is covered by
at least 20% of the average base coverage depth reads. Cumulative coverage is
linearly interpolated between nearest integer base read depths.
Target base coverage at
Nx
The percentage of target bases covered by at least
N reads.
Target bases with no strand
bias
The percentage of all target bases that did not show a bias toward forward or reverse
strand read alignments. An individual target base is considered to have read bias if it
has ≥10 reads and the percentage of forward or reverse reads to total reads is
greater than 70%. Target bases with <10 reads are considered to have no strand bias.
Percent end
‑
to
‑
end reads
The percentage of on
‑
target reads that fully cover their assigned amplicon (insert)
from 'end
‑
to
‑
end'. To allow for error, the effective ends of the amplicon region for
read alignment are within 2 bases of the actual ends of the region.
Example Coverage Analysis Report
The following is an example of a Coverage Analysis Report generated by the
coverageAnalysis plugin for an Ion AmpliSeq
™
DNA and fusions run. For a DNA and
fusions run, the DNA and fusion coverage results are viewable by clicking the
respective links in the Barcode Name column of the coverageAnalysis results table.
Appendix D
coverageAnalysis plugin in Genexus
™
Software
Example Coverage Analysis Report
D
Genexus
™
Integrated Sequencer User Guide
145
