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If you use plots from MultiQC in a publication or presentation, please cite:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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Tool Citations

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About MultiQC

This report was generated using MultiQC, version 1.16

You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

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Report generated on 2023-10-23, 11:13 +03 based on data in: /home/bar/runs/results.298674

General Statistics

Showing ³/₃ rows and ¹¹/₁₅ columns.

Sample Name	Vars	SNP	Indel	Ts/Tv	MNP	Error rate	M Non-Primary	M Reads Mapped	% Mapped	% Proper Pairs	% MapQ 0 Reads	M Total seqs	M Reads	M Reads Mapped	% Reads Mapped
U0a.bcf	10	10	0	1.50	0
U0a.cram.flagstat													4.5	4.4	99.3%
U0a.cram.stats						0.55%	0.0	4.4	99.3%	96.8%	4.8%	4.4

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: general_stats_table

Sort	Group	Column	Description	ID	Scale
\|\|	Bcftools Stats	Vars	Variations total	`number_of_records`	None
\|\|	Bcftools Stats	SNP	Variation SNPs	`number_of_SNPs`	None
\|\|	Bcftools Stats	Indel	Variation Insertions/Deletions	`number_of_indels`	None
\|\|	Bcftools Stats	Ts/Tv	Variant SNP transition / transversion ratio	`tstv`	None
\|\|	Bcftools Stats	MNP	Variation multinucleotide polymorphisms	`number_of_MNPs`	None
\|\|	Samtools	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`error_rate`	None
\|\|	Samtools	M Non-Primary	Non-primary alignments (millions)	`non-primary_alignments`	read_count
\|\|	Samtools	M Reads Mapped	Reads Mapped in the bam file (millions)	`reads_mapped`	read_count
\|\|	Samtools	% Mapped	% Mapped Reads	`reads_mapped_percent`	None
\|\|	Samtools	% Proper Pairs	% Properly Paired Reads	`reads_properly_paired_percent`	None
\|\|	Samtools	% MapQ 0 Reads	% of Reads that are Ambiguously Placed (MapQ=0)	`reads_MQ0_percent`	None
\|\|	Samtools	M Total seqs	Total sequences in the bam file (millions)	`raw_total_sequences`	read_count
\|\|	Samtools	M Reads	Total reads in the bam file (millions)	`flagstat_total`	read_count
\|\|	Samtools	M Reads Mapped	Reads Mapped in the bam file (millions)	`mapped_passed`	read_count
\|\|	Samtools	% Reads Mapped	% Reads Mapped in the bam file	`mapped_passed_pct`	None

resources 298674 log mqc png

U0A Mqc.Html

IGV Variant Inspector

Variants

file sizes 298674 log mqc png

Bcftools

Versions: 1.18, 1.18-14-g2c81697c

Bcftools contains utilities for variant calling and manipulating VCFs and BCFs.DOI: 10.1093/gigascience/giab008.

Variant Substitution Types

Variant Quality

Indel Distribution

Variant depths

Read depth support distribution for called variants

VEP

VEP Ensembl VEP determines the effect of your variants on genes, transcripts and protein sequences, as well as regulatory regions.DOI: 10.1186/s13059-016-0974-4.

General Statistics

Table showing general statistics of VEP annotaion run

Showing ¹/₁ rows and ⁷/₈ columns.

Sample Name	Overlapped regulatory features	Overlapped transcripts	Overlapped genes	Existing variants	Novel variants	Variants filtered out	Variants processed	Lines of input read
U0a_summary.html	0	1	1	10	0	0	10	10

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: vep-general-stats

Sort	Group	Column	Description	ID	Scale
\|\|	VEP	Overlapped regulatory features	Overlapped regulatory features	`Overlapped regulatory features`	None
\|\|	VEP	Overlapped transcripts	Overlapped transcripts	`Overlapped transcripts`	None
\|\|	VEP	Overlapped genes	Overlapped genes	`Overlapped genes`	None
\|\|	VEP	Existing variants	Existing variants	`Existing variants`	variants
\|\|	VEP	Novel variants	Novel variants	`Novel variants`	variants
\|\|	VEP	Variants filtered out	Variants filtered out	`Variants filtered out`	variants
\|\|	VEP	Variants processed	Variants processed	`Variants processed`	variants
\|\|	VEP	Lines of input read	Lines of input read	`Lines of input read`	None

Variant classes

Classes of variants found in the data.

Consequences

Predicted consequences of variations.

SIFT summary

SIFT variant effect prediction.

PolyPhen summary

PolyPhen variant effect prediction.

Variants by chromosome

Number of variants found on each chromosome.

Position in protein

Relative position of affected amino acids in protein.

Samtools

Versions: 1.18, 1.18-10-g007d83e

Samtools is a suite of programs for interacting with high-throughput sequencing data.DOI: 10.1093/bioinformatics/btp352.

Percent Mapped

Alignment metrics from samtools stats; mapped vs. unmapped reads.

For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

Alignment metrics

This module parses the output from samtools stats. All numbers in millions.

Samtools Flagstat

This module parses the output from samtools flagstat. All numbers in millions.

XY counts

Mapped reads per contig

The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Group	Software	Version
Bcftools	Bcftools	`1.18, 1.18-14-g2c81697c`
Samtools	Samtools	`1.18, 1.18-10-g007d83e`
annotation_sources	1000genomes	`phase3`
	COSMIC	`97`
	ClinVar	`202301`
	HGMD-PUBLIC	`20204`
	assembly	`GRCh38.p14`
	dbSNP	`154`
	gencode	`GENCODE 44`
	genebuild	`2014.post7`
	gnomADe	`r2.1.1`
	gnomADg	`3.1.2`
	polyphen	`2.2.3`
	regbuild	`1.0`
	sift	`6.2.1`
bedtools	bedtools	`2.31.0`
bwa	bwa	`0.7.17-r1198-dirty`
ensembl-vep	ensembl-vep	`110.1`
fastp	fastp	`0.23.4`
oneliner	oneliner	`1.0.0`

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General Statistics

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resources 298674 log mqc png

U0A Mqc.Html

file sizes 298674 log mqc png

Bcftools

Variant Substitution Types

Variant Quality

Indel Distribution

Variant depths

VEP

General Statistics Help

VEP General Statistics: Columns

Variant classes

Consequences

SIFT summary

PolyPhen summary

Variants by chromosome

Position in protein

Samtools

Percent Mapped Help

Alignment metrics

Samtools Flagstat

XY counts

Mapped reads per contig

Software Versions

v1.16

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General Statistics

Percent Mapped