Metric
Description
Uniformity of Base Coverage The percentage of reads with a depth of coverage ≥20% of the mean read coverage at
each position.
This metric is applicable to Ion AmpliSeq
™
HD library chemistry only.
Sample QC - RNA
Sequencing quality metrics of the sample RNA library.
Mapped Reads
The total number of final library reads that are aligned to the reference file for the
sample.
Mean Read Length (bp)
The average length, in base pairs, of the final library reads for the sample.
RNA Expression Ctrls
Detected
The number of expression control genes detected for the sample. This metric
measures the integrity of the RNA input used for library preparation.
Fusion panels include primer pairs that cover seven control housekeeping genes.
Mean AQ20 Read Length
The average length, in base pairs, of the final library reads with no more than 1%
error rate for the sample.
The average length, in base pairs, at which the accuracy rate is ≥99% for all aligned
reads of a library.
Read Length Histogram
The histogram presents all filtered and trimmed library reads that are reported in the
output BAM file (Y
‑
axis) and the mean read length in base pairs (X
‑
axis). The shape of
the histogram should closely resemble the library size distribution trace without the
adapter sequences.
The SNVs/Indels table lists the calls and other information for the SNV and INDEL
variants that are analyzed in each sample in a run.
To view the SNVs/Indels table, in the Results > Run Results screen, click the sample
name in the Sample Name column, then click SNVs/Indels in the left navigation
pane of the View Results screen.
The data displayed in the table depend on the assay that was used in the run. Filter
the results list in the table using the filtering tools. For more information, see “Filter
results“ on page 102. Click Export in the upper right corner of the screen to export
the results data in tabular format.
Column
Description
User Classifications
User-defined classification to selected from the list.
For more information, see “Create and assign variant classifications“ on page 102.
Locus
The chromosome and position of the detected variant.
Oncomine Variant
Class
The type of SNV or INDEL at the locus based on Oncomine
™
annotations:
• Hotspot
• Deleterious
This information is available if the Apply Oncomine Variant Annotations checkbox is selected
in the assay used in the run.
SNV/INDEL
results
Chapter 9
Review data and results
View sequencing results and run metrics
9
Genexus
™
Integrated Sequencer User Guide
95
