QC metric
Description
Pass threshold
Library QC – DNA
Amplicons With No Strand Bias The percentage of amplicons with a strand bias between 30% and
70%.
≥85.5
MAPD
MAPD (Median of the Absolute values of all Pairwise Differences)
is a quality metric that estimates coverage variability between
adjacent amplicons in copy number variant (CNV) analyses. A
MAPD value ≤0.5 indicates an acceptable level of coverage
variability.
≤0.5
Mapped Reads
The total number of reads mapped to the reference sequence.
≥1,100,000
Mean AQ20 read length (bp)
Average length, in base pairs, at which the error rate is ≤1% for all
aligned reads of the sample DNA library.
≥95
Percent Reads On Target
The percentage of reads mapped on target over total reads.
≥90
Sample Balance Factor
For a given sample in a PQ run, Sample Balance Factor = Number
of mapped reads / Mean number of mapped reads for four tested
samples A–D.
≥0.5
Uniformity Of Base Coverage
The percentage of bases having a depth of coverage ≥20% of the
mean coverage at each position.
≥95
Chapter 9
Review data and results
Verification runs
9
116
Genexus
™
Integrated Sequencer User Guide
