Sample meta information

Guide to MultiQC sections displaying sample meta information and pass/fail/warn metrics.

Introduction

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.

Example MultiQC report showing sample meta information.

Interpretation

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	biometrics	Minor contamination based on biometrics.
Major contamination	biometrics	Major contamination based on.
Fingerprint	biometrics	Pass: no unexpected matches/mismatches. NA: if no samples from the same patient to compare with. Fail: has unexpected matches/mismatches.
Sex mismatch	biometrics	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	sequence_qc	Percentage of noise.
N noise sites	sequence_qc	Number of sites contributing to noise.