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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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About MultiQC

This report was generated using MultiQC, version 1.3

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 2018-06-29, 20:32 based on data in: /projects/ps-epigen/outputs/setQCs/Set_138/4dceb7d4e23437466ebc58c2685c1b9d/libQCs

General Statistics

Showing ⁶⁴/₆₄ rows and ⁶/₉ columns.

Sample Name	M Reads Mapped	Insert Size	Mean Insert Size	% Aligned	% Dups	% GC	Length	% Failed	M Seqs
JYH_501_R1					11.9%	54%	75 bp	18%	0.7
JYH_501_R1.trim.PE2SE	1.4			99.2%
JYH_501_R1.trim.PE2SE.nodup	0.9	90 bp	123 bp
JYH_501_R2					11.9%	54%	75 bp	18%	0.7
JYH_502_R1					18.9%	53%	75 bp	18%	2.6
JYH_502_R1.trim.PE2SE	5.2			99.2%
JYH_502_R1.trim.PE2SE.nodup	3.4	97 bp	130 bp
JYH_502_R2					18.4%	53%	75 bp	18%	2.6
JYH_503_R1					21.2%	54%	75 bp	18%	6.2
JYH_503_R1.trim.PE2SE	12.2			99.3%
JYH_503_R1.trim.PE2SE.nodup	8.2	98 bp	134 bp
JYH_503_R2					20.3%	54%	75 bp	18%	6.2
JYH_504_R1					20.0%	53%	75 bp	18%	5.1
JYH_504_R1.trim.PE2SE	10.2			99.1%
JYH_504_R1.trim.PE2SE.nodup	6.7	97 bp	130 bp
JYH_504_R2					20.4%	53%	75 bp	18%	5.1
JYH_505_R1					22.1%	53%	75 bp	18%	6.1
JYH_505_R1.trim.PE2SE	12.1			99.2%
JYH_505_R1.trim.PE2SE.nodup	7.9	96 bp	129 bp
JYH_505_R2					22.4%	53%	75 bp	18%	6.1
JYH_506_R1					21.8%	53%	75 bp	18%	6.8
JYH_506_R1.trim.PE2SE	13.5			99.1%
JYH_506_R1.trim.PE2SE.nodup	8.8	92 bp	121 bp
JYH_506_R2					22.0%	52%	75 bp	18%	6.8
JYH_507_R1					31.5%	52%	75 bp	18%	15.2
JYH_507_R1.trim.PE2SE	30.0			98.9%
JYH_507_R1.trim.PE2SE.nodup	16.5	73 bp	95 bp
JYH_507_R2					31.2%	51%	75 bp	18%	15.2
JYH_508_R1					19.6%	51%	75 bp	18%	1.1
JYH_508_R1.trim.PE2SE	2.2			98.5%
JYH_508_R1.trim.PE2SE.nodup	1.2	59 bp	75 bp
JYH_508_R2					20.4%	51%	75 bp	18%	1.1
JYH_509_R1					37.7%	49%	75 bp	18%	1.7
JYH_509_R1.trim.PE2SE	3.4			99.0%
JYH_509_R1.trim.PE2SE.nodup	1.3	94 bp	127 bp
JYH_509_R2					37.3%	49%	75 bp	18%	1.7
JYH_510_R1					49.0%	49%	75 bp	18%	14.1
JYH_510_R1.trim.PE2SE	28.0			99.3%
JYH_510_R1.trim.PE2SE.nodup	10.1	98 bp	131 bp
JYH_510_R2					47.6%	49%	75 bp	18%	14.1
JYH_511_R1					43.8%	49%	75 bp	18%	6.1
JYH_511_R1.trim.PE2SE	12.1			99.2%
JYH_511_R1.trim.PE2SE.nodup	4.7	99 bp	132 bp
JYH_511_R2					42.7%	49%	75 bp	18%	6.1
JYH_512_R1					36.0%	49%	75 bp	18%	3.6
JYH_512_R1.trim.PE2SE	7.1			99.1%
JYH_512_R1.trim.PE2SE.nodup	2.9	92 bp	121 bp
JYH_512_R2					38.3%	49%	75 bp	18%	3.6
JYH_513_R1					43.2%	49%	75 bp	18%	6.2
JYH_513_R1.trim.PE2SE	12.3			99.2%
JYH_513_R1.trim.PE2SE.nodup	4.7	100 bp	131 bp
JYH_513_R2					42.9%	49%	75 bp	18%	6.2
JYH_514_R1					41.7%	49%	75 bp	18%	6.2
JYH_514_R1.trim.PE2SE	12.3			99.2%
JYH_514_R1.trim.PE2SE.nodup	4.9	97 bp	126 bp
JYH_514_R2					40.9%	48%	75 bp	18%	6.2
JYH_515_R1					53.6%	47%	75 bp	27%	11.5
JYH_515_R1.trim.PE2SE	22.7			99.0%
JYH_515_R1.trim.PE2SE.nodup	6.6	83 bp	105 bp
JYH_515_R2					52.9%	47%	75 bp	27%	11.5
JYH_516_R1					47.1%	47%	75 bp	9%	3.4
JYH_516_R1.trim.PE2SE	6.7			98.9%
JYH_516_R1.trim.PE2SE.nodup	2.1	66 bp	85 bp
JYH_516_R2					47.7%	47%	75 bp	18%	3.4

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Sort	Group	Column	Description	ID	Scale
\|\|	Samtools Flagstat	M Reads Mapped	Reads Mapped in the bam file (millions)	`mapped_passed`	read_count
\|\|	Picard	Insert Size	Median Insert Size, all read orientations (bp)	`summed_median`	None
\|\|	Picard	Mean Insert Size	Mean Insert Size, all read orientations (bp)	`summed_mean`	None
\|\|	Bowtie 2	% Aligned	overall alignment rate	`overall_alignment_rate`	None
\|\|	FastQC	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC	M Seqs	Total Sequences (millions)	`total_sequences`	read_count

Picard

Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

GC Coverage Bias

This plot shows bias in coverage across regions of the genome with varying GC content. A perfect library would be a flat line at y = 1.

Insert Size

Plot shows the number of reads at a given insert size. Reads with different orientations are summed.

Samtools

Samtools is a suite of programs for interacting with high-throughput sequencing data.

Samtools Flagstat

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

Bowtie 2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

This plot shows the number of reads aligning to the reference in different ways.
Please note that single mate alignment counts are halved to tally with pair counts properly.

There are 6 possible types of alignment: PE mapped uniquely: Pair has only one occurence in the reference genome. PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair. PE one mate mapped uniquely: One read of a pair has one occurence. PE multimapped: Pair has multiple occurence. PE one mate multimapped: One read of a pair has multiple occurence. PE neither mate aligned: Pair has no occurence.

FastQ Screen

FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

FastQC

FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

Sequence Quality Histograms

The mean quality value across each base position in the read. See the FastQC help.

Per Sequence Quality Scores

The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.

Per Base Sequence Content

The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.

Click a sample row to see a line plot for that dataset.

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%T: -

%C: -

%A: -

%G: -

Per Sequence GC Content

The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.

Per Base N Content

The percentage of base calls at each position for which an N was called. See the FastQC help.

Sequence Length Distribution

All samples have sequences of a single length (75bp).

Sequence Duplication Levels

The relative level of duplication found for every sequence. See the FastQC help.

Overrepresented sequences

The total amount of overrepresented sequences found in each library. See the FastQC help for further information.

32 samples had less than 1% of reads made up of overrepresented sequences

Adapter Content

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.

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About MultiQC

General Statistics

General Statistics: Columns

Picard

GC Coverage Bias

Insert Size

Samtools

Samtools Flagstat

Bowtie 2

FastQ Screen

FastQC

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Rollover for sample name

Per Sequence GC Content

Per Base N Content

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

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