coverageAnalysis plugin in
Genexus
™
Software
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Reads statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
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Example Coverage Analysis Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
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Example charts generated by the coverageAnalysis plugin . . . . . . . . . . . . . . . . 147
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Output files generated by the coverageAnalysis plugin . . . . . . . . . . . . . . . . . . . 148
Use the coverageAnalysis plugin to view statistics and graphs that describe the level
of sequence coverage produced for targeted genomic regions. The results in the
Summary screen for a run analyzed with the plugin vary based on the library type
that you select when you configure the plugin. You can export some charts as
graphics, such as the Amplicon Coverage Chart and the Reference Coverage Chart.
Reads statistics
The library type determines which statistics are presented. The following tables
describe the statistics that are generated by the coverageAnalysis plugin. The statistics
that are displayed in your report depend on the type of library that is used in your
sequencing experiment. Definitions are in tooltips. Almost every statistic, plot, link,
and functional widget in the report provides tooltips with definitions. Hover over a
heading or description in the report to view the tooltip.
General statistics
Statistic
Description
Number of mapped reads
The total number of reads mapped to the reference genome.
Percent reads on target
The percentage of filtered reads mapped to any targeted region relative to all reads
mapped to the reference. If no target regions file is specified, this value will be the
percentage of reads passing uniquely mapped and/or non
‑
duplicate filters, or 100%
if no filters were specified. A read is considered on target if at least one aligned base
overlaps at least one target region. A read that overlaps a targeted region but where
only flanking sequence is aligned, for example, due to poor matching of 5' bases of
the read, is not counted.
Amplicon read coverage statistics
The following statistics describe the reads that are assigned to specific amplicons. Each sequence read is assigned to
exactly one of the amplicons specified by the targets file. If a read spans multiple amplicon targets, the target region
that the reads covers most is assigned. In the even of a tie, the target that is the closest to the 3' end is assigned.
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Genexus
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Integrated Sequencer User Guide
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