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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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.

Sample Name	Reads	Reads mapped	% Reads mapped	% Aligned
03_align				96.5%
SNF2KO_01	0.6M	0.5M	97.5%	97.2%
SNF2KO_02	0.6M	0.6M	97.2%	96.7%
SNF2KO_03	0.6M	0.5M	97.1%	96.7%
SNF2KO_04	0.6M	0.6M	98.6%	98.2%
SNF2KO_05	0.6M	0.5M	97.0%	96.6%
SNF2KO_06	0.6M	0.5M	96.9%	96.5%
SNF2KO_07	0.6M	0.5M	96.8%	96.4%
SNF2KO_08	0.6M	0.6M	96.8%	96.2%
SNF2KO_09	0.6M	0.5M	97.1%	96.8%
SNF2KO_10	0.6M	0.5M	97.1%	96.8%
SNF2KO_11	0.6M	0.5M	96.5%	96.1%
SNF2KO_12	0.6M	0.5M	97.3%	97.0%
WT_01	0.6M	0.6M	96.9%	96.4%
WT_02	0.6M	0.6M	97.4%	97.0%
WT_03	0.6M	0.6M	96.5%	95.9%
WT_04	0.6M	0.6M	97.5%	97.2%
WT_05	0.6M	0.6M	97.3%	96.9%
WT_06	0.6M	0.6M	97.8%	97.5%
WT_07	0.6M	0.6M	97.4%	97.0%
WT_08	0.6M	0.6M	97.4%	96.9%
WT_09	0.6M	0.6M	97.6%	97.2%
WT_10	0.6M	0.6M	97.2%	96.5%
WT_11	0.6M	0.6M	97.5%	97.0%
WT_12	0.6M	0.6M	97.0%	96.5%

Sort	Group	Column	Description	ID	Scale
\|\|	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`
\|\|	Bowtie 2 / HiSAT2	% Aligned	overall alignment rate	`bowtie_2_hisat2-overall_alignment_rate`

Sample Name	Total Reads	Total Passed QC	Mapped	Secondary Alignments	Duplicates	Paired in Sequencing	Properly Paired	Self and mate mapped	Singletons	Mate mapped to diff chr	Diff chr (mapQ >= 5)
SNF2KO_01	0.6M	0.6M	0.5M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
SNF2KO_02	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
SNF2KO_03	0.6M	0.6M	0.5M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
SNF2KO_04	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
SNF2KO_05	0.6M	0.6M	0.5M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
SNF2KO_06	0.6M	0.6M	0.5M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
SNF2KO_07	0.6M	0.6M	0.5M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
SNF2KO_08	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
SNF2KO_09	0.6M	0.6M	0.5M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
SNF2KO_10	0.6M	0.6M	0.5M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
SNF2KO_11	0.6M	0.6M	0.5M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
SNF2KO_12	0.6M	0.6M	0.5M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
WT_01	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
WT_02	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
WT_03	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
WT_04	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
WT_05	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
WT_06	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
WT_07	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
WT_08	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
WT_09	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
WT_10	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
WT_11	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
WT_12	0.6M	0.6M	0.6M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M

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
\|\|	Secondary Alignments	Secondary Alignments	`secondary_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

Sample Name	Total Reads	Total Passed QC	Mapped	Secondary Alignments	Duplicates	Paired in Sequencing	Properly Paired	Self and mate mapped	Singletons	Mate mapped to diff chr	Diff chr (mapQ >= 5)
SNF2KO_01	100.0%	100.0%	97.5%	10.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
SNF2KO_02	100.0%	100.0%	97.2%	15.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
SNF2KO_03	100.0%	100.0%	97.1%	10.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
SNF2KO_04	100.0%	100.0%	98.6%	20.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
SNF2KO_05	100.0%	100.0%	97.0%	11.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
SNF2KO_06	100.0%	100.0%	96.9%	10.7%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
SNF2KO_07	100.0%	100.0%	96.8%	10.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
SNF2KO_08	100.0%	100.0%	96.8%	13.7%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
SNF2KO_09	100.0%	100.0%	97.1%	10.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
SNF2KO_10	100.0%	100.0%	97.1%	10.5%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
SNF2KO_11	100.0%	100.0%	96.5%	10.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
SNF2KO_12	100.0%	100.0%	97.3%	9.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
WT_01	100.0%	100.0%	96.9%	13.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
WT_02	100.0%	100.0%	97.4%	14.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
WT_03	100.0%	100.0%	96.5%	13.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
WT_04	100.0%	100.0%	97.5%	13.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
WT_05	100.0%	100.0%	97.3%	14.2%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
WT_06	100.0%	100.0%	97.8%	12.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
WT_07	100.0%	100.0%	97.4%	13.5%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
WT_08	100.0%	100.0%	97.4%	14.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
WT_09	100.0%	100.0%	97.6%	13.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
WT_10	100.0%	100.0%	97.2%	18.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
WT_11	100.0%	100.0%	97.5%	16.5%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
WT_12	100.0%	100.0%	97.0%	14.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%

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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`
\|\|	Secondary Alignments	Secondary Alignments	`secondary_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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