Sample meta information
Guide to MultiQC sections displaying sample meta information and pass/fail/warn metrics.
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Guide to MultiQC sections displaying sample meta information and pass/fail/warn metrics.
Last updated
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At the top of the MultiQC report are one or two tables showing some per-sample information. One table is for plasma samples and another is for buffy-coat samples; so only one table may show up depending on your sample composition.
In the above figure you'll notice that most columns are highlighted as either red, yellow or green, which indicates if the metric fails, is borderline, or passes the thresholds set for each, respectively. This allows you to quickly glance at all samples to see where potential issues are. Below are the descriptions for each column and were the data was obtained from.
Column name
Source
Description
cmoSampleName
LIMS
The sample name.
Library input
LIMS
The library input.
Library yield
LIMS
The library yield.
Pool input
LIMS
The pool input.
Raw cov. (pool A)
MEAN_TARGET_COVERAGE column in the output file produced by GATK-CollectHsMetrics (uncollapsed BAM, pool A).
The mean sequencing coverage over target regions in Pool A.
Raw cov. (pool B)
MEAN_TARGET_COVERAGE column in the output file produced by GATK-CollectHsMetrics (uncollapsed BAM, pool B).
The mean sequencing coverage over target regions in Pool B.
Duplex target cov.
MEAN_TARGET_COVERAGE column in the output file produced by GATK-CollectHsMetrics (duplex BAM, pool A).
Average coverage over pool A targets in the duplex BAM.
Minor contamination
Minor contamination based on biometrics.
Major contamination
Major contamination based on.
Fingerprint
Pass: no unexpected matches/mismatches. NA: if no samples from the same patient to compare with. Fail: has unexpected matches/mismatches.
Sex mismatch
Do the sample's predicted and expected sex mismatch?
Ins. size (MODE)
MODE_INSERT_SIZE column from GATK-CollectHsMetrics (Duplex BAM).
The most frequently occurring insert size.
N reads
TOTAL_READS column in the output file produced by GATK-CollectHsMetrics (uncollapsed BAM).
Total reads sequenced (uncollapsed)
% Aligned
PCT_PF_UQ_READS_ALIGNED column in the output file produced by GATK-CollectHsMetrics (uncollapsed BAM).
Percentage of reads aligned to the genome.
% Noise
Percentage of noise.
N noise sites
Number of sites contributing to noise.
