MultiQC Report

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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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About MultiQC

This report was generated using MultiQC, version 1.32

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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

MultiQC is developed by Seqera.

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

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Report generated on 2025-12-02, 10:58 CET based on data in: /home/flalom/project/course_data/alignments

General Statistics

Showing ²/₂ rows and ⁴/₆ columns.

Sample Name	Fold Enrichment	Median Target Coverage	Target Bases ≥ 30X	Reads	Reads mapped	% Reads mapped
normal.recal	22X	72.0X	83%	12.7M	12.7M	99.4%
tumor.recal	23X	95.0X	87%	16.7M	16.6M	99.5%

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

Sort	Group	Column	Description	ID	Scale
\|\|	Picard: HsMetrics	Fold Enrichment	Fold Enrichment	`picard_hsmetrics-FOLD_ENRICHMENT`
\|\|	Picard: HsMetrics	Median Target Coverage	The median coverage of reads that mapped to target regions of an experiment.	`picard_hsmetrics-MEDIAN_TARGET_COVERAGE`
\|\|	Picard: HsMetrics	Target Bases ≥ 30X	Percent of target bases with coverage ≥ 30X	`picard_hsmetrics-picard_target_bases_30X`
\|\|	Samtools: flagstat	Reads	Total reads in the bam file (millions)	`samtools_flagstat-flagstat_total`	read_count
\|\|	Samtools: flagstat	Reads mapped	Reads mapped in the bam file (millions)	`samtools_flagstat-mapped_passed`	read_count
\|\|	Samtools: flagstat	% Reads mapped	% Reads mapped in the bam file	`samtools_flagstat-mapped_passed_pct`

Picard

Tools for manipulating high-throughput sequencing data.http://broadinstitute.github.io/picard

Hybrid-selection metrics

Parsed from Picard HsMetrics tool that takes a SAM/BAM file input and collects metrics that are specific for sequence datasets generated through hybrid-selection. Hybrid-selection (HS) is the most commonly used technique to capture exon-specific sequences for targeted sequencing experiments such as exome sequencing.

Showing ²/₂ rows and ²⁴/₂₉ columns.

Sample Name	At dropout	Bait design efficiency	Bait territory	Fold 80 base penalty	Fold enrichment	Gc dropout	Het SNP q	Het SNP sensitivity	Near-bait bases	Off-bait bases	On-bait bases	On-target bases	Usable bases on-bait	Usable bases on-target	PF bases	PF bases aligned	PF reads	Selected bases	PF unique reads	PF unique bases aligned	PF unique reads aligned	Total reads	Max target coverage	Mean bait coverage	Mean target coverage	Median target coverage	On-bait vs selected	Target territory	Zero coverage targets
normal.recal	0.0	1.0	6683920.0	2.5	22.1	6.1	14.0	1.0	400.4Mb	126.6Mb	732.3Mb	563.8Mb	57.5%	44.3%	1273.3Mb	1259.3Mb	12.7M	89.9%	11.3M	1120.4Mb	11.3M	12.7M	1417.0	109.6	84.3	72.0	0.6	6683920.0	1.2%
tumor.recal	0.2	1.0	6683920.0	2.6	22.8	4.1	15.0	1.0	511.1Mb	150.8Mb	987.0Mb	768.0Mb	59.2%	46.1%	1666.3Mb	1648.9Mb	16.7M	90.9%	14.8M	1462.8Mb	14.7M	16.7M	2913.0	147.7	114.9	95.0	0.7	6683920.0	1.2%

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

Sort	Column	Description	ID	Scale
\|\|	At dropout	A measure of how undercovered <= 50% GC regions are relative to the mean.	`hsmetrics-AT_DROPOUT`
\|\|	Bait design efficiency	Target territory / bait territory. 1 == perfectly efficient, 0.5 = half of baited bases are not target.	`hsmetrics-BAIT_DESIGN_EFFICIENCY`
\|\|	Bait territory	The number of bases which have one or more baits on top of them.	`hsmetrics-BAIT_TERRITORY`
\|\|	Fold 80 base penalty	The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.	`hsmetrics-FOLD_80_BASE_PENALTY`
\|\|	Fold enrichment	The fold by which the baited region has been amplified above genomic background.	`hsmetrics-FOLD_ENRICHMENT`
\|\|	Gc dropout	A measure of how undercovered >= 50% GC regions are relative to the mean.	`hsmetrics-GC_DROPOUT`
\|\|	Het SNP q	The Phred Scaled Q Score of the theoretical HET SNP sensitivity.	`hsmetrics-HET_SNP_Q`
\|\|	Het SNP sensitivity	The theoretical HET SNP sensitivity.	`hsmetrics-HET_SNP_SENSITIVITY`
\|\|	Near-bait bases	The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region.	`hsmetrics-NEAR_BAIT_BASES`	base_count
\|\|	Off-bait bases	The number of PF aligned bases that mapped to neither on or near a bait.	`hsmetrics-OFF_BAIT_BASES`	base_count
\|\|	On-bait bases	The number of PF aligned bases that mapped to a baited region of the genome.	`hsmetrics-ON_BAIT_BASES`	base_count
\|\|	On-target bases	The number of PF aligned bases that mapped to a targeted region of the genome.	`hsmetrics-ON_TARGET_BASES`	base_count
\|\|	Usable bases on-bait	The number of aligned, de-duped, on-bait bases out of the PF bases available.	`hsmetrics-PCT_USABLE_BASES_ON_BAIT`
\|\|	Usable bases on-target	The number of aligned, de-duped, on-target bases out of the PF bases available.	`hsmetrics-PCT_USABLE_BASES_ON_TARGET`
\|\|	PF bases	The number of bases in the PF reads.	`hsmetrics-PF_BASES`	base_count
\|\|	PF bases aligned	The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.	`hsmetrics-PF_BASES_ALIGNED`	base_count
\|\|	PF reads	The number of reads that pass the vendor's filter.	`hsmetrics-PF_READS`	read_count
\|\|	Selected bases	On+Near Bait Bases / PF Bases Aligned.	`hsmetrics-PCT_SELECTED_BASES`
\|\|	PF unique reads	The number of PF reads that are not marked as duplicates.	`hsmetrics-PF_UNIQUE_READS`	read_count
\|\|	PF unique bases aligned	The number of bases in the PF aligned reads that are mapped to a reference base. Accounts for clipping and gaps.	`hsmetrics-PF_UQ_BASES_ALIGNED`	base_count
\|\|	PF unique reads aligned	The number of PF unique reads that are aligned with mapping score > 0 to the reference genome.	`hsmetrics-PF_UQ_READS_ALIGNED`	read_count
\|\|	Total reads	The total number of reads in the SAM or BAM file examine.	`hsmetrics-TOTAL_READS`	read_count
\|\|	Max target coverage	The maximum coverage of reads that mapped to target regions of an experiment.	`hsmetrics-MAX_TARGET_COVERAGE`
\|\|	Mean bait coverage	The mean coverage of all baits in the experiment.	`hsmetrics-MEAN_BAIT_COVERAGE`
\|\|	Mean target coverage	The mean coverage of targets.	`hsmetrics-MEAN_TARGET_COVERAGE`
\|\|	Median target coverage	The median coverage of targets.	`hsmetrics-MEDIAN_TARGET_COVERAGE`
\|\|	On-bait vs selected	The percentage of on+near bait bases that are on as opposed to near.	`hsmetrics-ON_BAIT_VS_SELECTED`
\|\|	Target territory	The unique number of target bases in the experiment where target is usually exons etc.	`hsmetrics-TARGET_TERRITORY`
\|\|	Zero coverage targets	The fraction of targets that did not reach coverage=1 over any base.	`hsmetrics-ZERO_CVG_TARGETS_PCT`

Hybrid-selection target coverage

The percentage of all target bases with at least x fold coverage.

Created with MultiQC

Hybrid-selection penalty

The "hybrid selection penalty" incurred to get 80% of target bases to a given coverage.

Can be used with the following formula:

required_aligned_bases = bait_size_bp * desired_coverage * hs_penalty

Created with MultiQC

Samtools

Toolkit for interacting with BAM/CRAM files.http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

Flagstat

This module parses the output from samtools flagstat

Created with MultiQC

Sample Name	Total Reads	Total Passed QC	Mapped	Supplementary Alignments	Duplicates	Paired in Sequencing	Properly Paired	Self and mate mapped	Singletons	Mate mapped to diff chr	Diff chr (mapQ >= 5)
normal.recal	12.7M	12.7M	12.7M	0.0M	1.4M	12.7M	12.5M	12.6M	0.1M	0.0M	0.0M
tumor.recal	16.7M	16.7M	16.6M	0.0M	1.9M	16.7M	16.4M	16.5M	0.1M	0.0M	0.0M

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samtools-flagstat-table_table

Sort	Column	Description	ID	Scale
\|\|	Total Reads	Total Reads	`flagstat_total`	read_count
\|\|	Total Passed QC	Total Passed QC	`total_passed`	read_count
\|\|	Mapped	Mapped	`mapped_passed`	read_count
\|\|	Supplementary Alignments	Supplementary Alignments	`supplementary_passed`	read_count
\|\|	Duplicates	Duplicates	`duplicates_passed`	read_count
\|\|	Paired in Sequencing	Paired in Sequencing	`paired_in_sequencing_passed`	read_count
\|\|	Properly Paired	Properly Paired	`properly_paired_passed`	read_count
\|\|	Self and mate mapped	Reads with itself and mate mapped	`with_itself_and_mate_mapped_passed`	read_count
\|\|	Singletons	Singletons	`singletons_passed`	read_count
\|\|	Mate mapped to diff chr	Mate mapped to different chromosome	`with_mate_mapped_to_a_different_chr_passed`	read_count
\|\|	Diff chr (mapQ >= 5)	Mate mapped to different chromosome (mapQ >= 5)	`with_mate_mapped_to_a_different_chr_mapQ_5__passed`	read_count

Flagstat: Percentage of total

This module parses the output from samtools flagstat

Created with MultiQC

Sample Name	Total Reads	Total Passed QC	Mapped	Supplementary Alignments	Duplicates	Paired in Sequencing	Properly Paired	Self and mate mapped	Singletons	Mate mapped to diff chr	Diff chr (mapQ >= 5)
normal.recal	100.0%	100.0%	99.4%	0.1%	11.0%	99.9%	98.2%	98.8%	0.6%	0.2%	0.1%
tumor.recal	100.0%	100.0%	99.5%	0.1%	11.2%	99.9%	98.4%	98.8%	0.5%	0.1%	0.1%

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samtools-flagstat-pct-table_table

Sort	Column	Description	ID
\|\|	Total Reads	Total Reads	`flagstat_total_pct`
\|\|	Total Passed QC	Total Passed QC	`total_passed_pct`
\|\|	Mapped	Mapped	`mapped_passed_pct`
\|\|	Supplementary Alignments	Supplementary Alignments	`supplementary_passed_pct`
\|\|	Duplicates	Duplicates	`duplicates_passed_pct`
\|\|	Paired in Sequencing	Paired in Sequencing	`paired_in_sequencing_passed_pct`
\|\|	Properly Paired	Properly Paired	`properly_paired_passed_pct`
\|\|	Self and mate mapped	Self and mate mapped	`with_itself_and_mate_mapped_passed_pct`
\|\|	Singletons	Singletons	`singletons_passed_pct`
\|\|	Mate mapped to diff chr	Mate mapped to diff chr	`with_mate_mapped_to_a_different_chr_passed_pct`
\|\|	Diff chr (mapQ >= 5)	Diff chr (mapQ >= 5)	`with_mate_mapped_to_a_different_chr_mapQ_5__passed_pct`

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