MultiQC Report

v1.25.1

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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 1.25.1

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/MultiQC/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

MultiQC is developed by:

Sort	Group	Column	Description	ID	Scale
\|\|	Custom content: DupRadar	dupInt	Intercept value from DupRadar	`custom_content_dupradar-dupRadar_intercept`
\|\|	Picard: Mark Duplicates	Duplication	Mark Duplicates - Percent Duplication	`picard_mark_duplicates-PERCENT_DUPLICATION`
\|\|	QualiMap: RNASeq	5'-3' bias	5'-3' bias	`qualimap_rnaseq-5_3_bias`
\|\|	QualiMap: RNASeq	M Aligned	Reads Aligned (millions)	`qualimap_rnaseq-reads_aligned`	read_count
\|\|	RSEM	% Alignable, M	% Alignable reads, millions	`rsem-alignable_percent`
\|\|	RSeQC: Bam Stat	Proper Pairs	% Reads mapped in proper pairs	`rseqc_bam_stat-proper_pairs_percent`
\|\|	Samtools: stats	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`samtools_stats-error_rate`
\|\|	Samtools: stats	Non-primary	Non-primary alignments (millions)	`samtools_stats-non_primary_alignments`	read_count
\|\|	Samtools: stats	Reads mapped	Reads mapped in the bam file (millions)	`samtools_stats-reads_mapped`	read_count
\|\|	Samtools: stats	% Mapped	% Mapped reads	`samtools_stats-reads_mapped_percent`
\|\|	Samtools: stats	% Proper pairs	% Properly paired reads	`samtools_stats-reads_properly_paired_percent`
\|\|	Samtools: stats	% MapQ 0 reads	% of reads that are ambiguously placed (MapQ=0)	`samtools_stats-reads_MQ0_percent`
\|\|	Samtools: stats	Total seqs	Total sequences in the bam file (millions)	`samtools_stats-raw_total_sequences`	read_count
\|\|	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`
\|\|	FastQC (raw)	Dups	% duplicate reads	`fastqc_raw-percent_duplicates`
\|\|	FastQC (raw)	GC	Average % GC content	`fastqc_raw-percent_gc`
\|\|	FastQC (raw)	Avg len	Average read length	`fastqc_raw-avg_sequence_length`
\|\|	FastQC (raw)	Median len	Median read length	`fastqc_raw-median_sequence_length`
\|\|	FastQC (raw)	Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`fastqc_raw-percent_fails`
\|\|	FastQC (raw)	Seqs	Total sequences (millions)	`fastqc_raw-total_sequences`
\|\|	Cutadapt	Trimmed bases	% total base pairs trimmed	`cutadapt-percent_trimmed`
\|\|	FastQC (trimmed)	Dups	% duplicate reads	`fastqc_trimmed-percent_duplicates`
\|\|	FastQC (trimmed)	GC	Average % GC content	`fastqc_trimmed-percent_gc`
\|\|	FastQC (trimmed)	Avg len	Average read length	`fastqc_trimmed-avg_sequence_length`
\|\|	FastQC (trimmed)	Median len	Median read length	`fastqc_trimmed-median_sequence_length`
\|\|	FastQC (trimmed)	Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`fastqc_trimmed-percent_fails`
\|\|	FastQC (trimmed)	Seqs	Total sequences (millions)	`fastqc_trimmed-total_sequences`

Sample	Status	Strand inference method	Provided strandedness	Inferred strandedness	Sense (%)	Antisense (%)	Unstranded (%)
NCONTROL_REP1	pass	RSeQC	auto	reverse	6.7	89.4	3.9
NCONTROL_REP1	pass	Salmon	auto	reverse	4.1	95.9	0.0
NCONTROL_REP2	pass	RSeQC	auto	reverse	6.6	89.5	3.9
NCONTROL_REP2	pass	Salmon	auto	reverse	3.6	96.4	0.0
NCONTROL_REP3	pass	RSeQC

Sample

NCONTROL_REP1

pass

RSeQC

auto

reverse

6.7

89.4

3.9

NCONTROL_REP1

pass

Salmon

auto

reverse

4.1

95.9

0.0

NCONTROL_REP2

pass

RSeQC

auto

reverse

6.6

89.5

3.9

NCONTROL_REP2

pass

Salmon

auto

reverse

3.6

96.4

0.0

NCONTROL_REP3

pass

RSeQC

Sample Name	dupInt	Duplication	5'-3' bias	M Aligned	% Alignable, M	Proper Pairs	Error rate	Non-primary	Reads mapped	% Mapped	% Proper pairs	% MapQ 0 reads	Total seqs	Reads	Reads mapped	% Reads mapped	Dups	GC	Avg len	Median len	Failed	Seqs	Trimmed bases	Dups	GC	Avg len	Median len	Failed	Seqs
NCONTROL_REP1	0.1	41.2%	1.05	16.8M	23.5%	13.7%	0.61%	15.9M	33.6M	28.3%	28.3%	1.1%	118.8M	134.7M	49.5M	36.8%
NCONTROL_REP1_1																	90.5%	52.0%	75bp	76bp	45%	59.8M	0.5%	90.5%	52.0%	75bp	76bp	45%	59.4M
NCONTROL_REP1_2																	88.4%	52.0%	75bp	76bp	45%	59.8M	0.9%	88.7%	52.0%	75bp	76bp	45%	59.4M
NCONTROL_REP2	0.1	43.0%	1.03	16.5M	19.4%	11.3%	0.63%	16.6M	33.1M	24.0%	24.0%	1.0%	137.9M	154.5M	49.7M	32.1%
NCONTROL_REP2_1																	92.1%	53.0%	75bp	76bp	45%	69.5M	0.6%	92.1%	52.0%	75bp	76bp	45%	69.0M
NCONTROL_REP2_2																	90.5%	53.0%	75bp	76bp	45%	69.5M	0.9%	90.7%	53.0%	75bp	76bp	45%	69.0M
NCONTROL_REP3	0.1	41.2%	0.98	13.7M	19.7%	11.3%	0.65%	15.8M	27.4M	23.8%	23.8%	1.2%	115.2M	131.0M	43.2M	33.0%
NCONTROL_REP3_1																	92.3%	52.0%	75bp	76bp	45%	57.9M	0.5%	92.3%	52.0%	75bp	76bp	45%	57.6M
NCONTROL_REP3_2																	90.6%	53.0%	75bp	76bp	45%	57.9M	0.9%	90.8%	53.0%	75bp	76bp	45%	57.6M
PCONTROL_REP1	0.1	42.5%	1.05	15.7M	20.7%	11.8%	0.64%	15.6M	31.5M	25.1%	25.1%	1.1%	125.6M	141.2M	47.1M	33.4%
PCONTROL_REP1_1																	92.0%	53.0%	75bp	76bp	45%	63.1M	0.4%	92.0%	53.0%	75bp	76bp	45%	62.8M
PCONTROL_REP1_2																	90.1%	53.0%	75bp	76bp	45%	63.1M	0.8%	90.3%	53.0%	75bp	76bp	45%	62.8M
PCONTROL_REP2	0.1	43.1%	1.05	12.9M	18.7%	11.2%	0.71%	16.2M	25.9M	24.6%	24.6%	1.2%	105.3M	121.5M	42.1M	34.6%
PCONTROL_REP2_1																	91.8%	53.0%	74bp	76bp	45%	54.1M	1.4%	91.7%	53.0%	75bp	76bp	45%	52.6M
PCONTROL_REP2_2																	89.4%	54.0%	74bp	76bp	45%	54.1M	2.1%	89.6%	54.0%	75bp	76bp	45%	52.6M
PCONTROL_REP3	0.1	42.9%	1.06	12.9M	17.9%	10.3%	0.67%	15.1M	25.7M	21.9%	21.9%	1.0%	117.2M	132.3M	40.8M	30.8%
PCONTROL_REP3_1																	93.0%	53.0%	75bp	76bp	45%	59.2M	0.6%	93.0%	53.0%	75bp	76bp	45%	58.6M
PCONTROL_REP3_2																	90.8%	54.0%	75bp	76bp	45%	59.2M	1.1%	91.0%	54.0%	75bp	76bp	45%	58.6M
SAV_REP1	0.1	41.2%	1.05	10.7M	18.3%	10.8%	0.62%	11.3M	21.5M	22.2%	22.2%	0.9%	96.7M	108.0M	32.8M	30.3%
SAV_REP1_1																	92.3%	53.0%	75bp	76bp	45%	48.6M	0.4%	92.3%	53.0%	75bp	76bp	45%	48.4M
SAV_REP1_2																	90.9%	54.0%	75bp	76bp	45%	48.6M	0.8%	91.1%	53.0%	75bp	76bp	45%	48.4M
SAV_REP2	0.1	38.0%	1.04	13.8M	21.4%	13.4%	0.65%	14.4M	27.6M	26.4%	26.4%	1.1%	104.2M	118.6M	42.0M	35.4%
SAV_REP2_1																	90.4%	52.0%	75bp	76bp	45%	52.4M	0.4%	90.4%	52.0%	75bp	76bp	45%	52.1M
SAV_REP2_2																	88.8%	53.0%	75bp	76bp	45%	52.4M	0.8%	89.0%	53.0%	75bp	76bp	45%	52.1M
SAV_REP3	0.1	41.8%	1.04	10.5M	15.9%	9.6%	0.66%	10.6M	20.9M	19.5%	19.5%	0.9%	107.3M	117.9M	31.6M	26.8%
SAV_REP3_1																	93.1%	53.0%	75bp	76bp	45%	53.9M	0.4%	93.1%	53.0%	75bp	76bp	45%	53.6M
SAV_REP3_2																	91.6%	54.0%	75bp	76bp	45%	53.9M	0.9%	91.8%	54.0%	75bp	76bp	45%	53.6M

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