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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 1.0.dev0

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 2018-03-02, 17:03 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HJJT3BGX5/merged

General Statistics

Showing ⁴⁰/₄₀ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
HJJT3BGX5_n01_ir108_3bs_11_1	59.8%	53%	75 bp	25%	15.3
HJJT3BGX5_n01_ir108_3bs_11_2	53.5%	52%	75 bp	33%	9.2
HJJT3BGX5_n01_ir108_3bs_12_1	67.0%	53%	75 bp	25%	25.1
HJJT3BGX5_n01_ir108_3bs_12_2	58.7%	54%	75 bp	25%	3.7
HJJT3BGX5_n01_ir108_3bs_1_1	64.7%	53%	75 bp	25%	9.4
HJJT3BGX5_n01_ir108_3bs_1_2	54.3%	54%	75 bp	33%	6.7
HJJT3BGX5_n01_ir108_3bs_6_1	65.7%	54%	75 bp	25%	13.3
HJJT3BGX5_n01_ir108_3bs_6_2	63.3%	54%	75 bp	25%	8.9
HJJT3BGX5_n01_ir108_3bs_9_1	52.7%	53%	75 bp	25%	6.1
HJJT3BGX5_n01_ir108_3bs_9_2	57.5%	53%	75 bp	33%	11.2
HJJT3BGX5_n01_ir108_4bs_11_1	61.0%	53%	75 bp	25%	10.2
HJJT3BGX5_n01_ir108_4bs_11_2	62.3%	54%	75 bp	25%	6.2
HJJT3BGX5_n01_ir108_4bs_12_1	58.3%	53%	75 bp	25%	7.9
HJJT3BGX5_n01_ir108_4bs_12_2	67.4%	53%	75 bp	25%	15.8
HJJT3BGX5_n01_ir108_4bs_1_1	58.7%	53%	75 bp	25%	6.9
HJJT3BGX5_n01_ir108_4bs_1_2	62.0%	54%	75 bp	25%	6.0
HJJT3BGX5_n01_ir108_4bs_6_1	67.2%	53%	75 bp	25%	12.7
HJJT3BGX5_n01_ir108_4bs_6_2	66.5%	54%	75 bp	25%	9.6
HJJT3BGX5_n01_ir108_4bs_9_1	61.7%	53%	75 bp	25%	6.7
HJJT3BGX5_n01_ir108_4bs_9_2	60.6%	53%	75 bp	25%	6.2
HJJT3BGX5_n01_ir64_3bs_11_1	56.4%	52%	75 bp	25%	14.5
HJJT3BGX5_n01_ir64_3bs_11_2	47.1%	52%	75 bp	25%	6.5
HJJT3BGX5_n01_ir64_3bs_12_1	61.5%	52%	75 bp	25%	16.5
HJJT3BGX5_n01_ir64_3bs_12_2	56.6%	52%	75 bp	33%	12.1
HJJT3BGX5_n01_ir64_3bs_1_1	62.9%	53%	75 bp	25%	16.2
HJJT3BGX5_n01_ir64_3bs_1_2	55.7%	52%	75 bp	25%	6.7
HJJT3BGX5_n01_ir64_3bs_6_1	68.9%	54%	75 bp	25%	10.1
HJJT3BGX5_n01_ir64_3bs_6_2	79.1%	53%	75 bp	25%	8.6
HJJT3BGX5_n01_ir64_3bs_9_1	57.2%	52%	75 bp	25%	8.9
HJJT3BGX5_n01_ir64_3bs_9_2	56.5%	52%	75 bp	25%	8.1
HJJT3BGX5_n01_ir64_4bs_11_1	66.3%	53%	75 bp	25%	15.2
HJJT3BGX5_n01_ir64_4bs_11_2	56.9%	53%	75 bp	25%	8.1
HJJT3BGX5_n01_ir64_4bs_12_1	65.0%	53%	75 bp	25%	25.2
HJJT3BGX5_n01_ir64_4bs_12_2	67.1%	53%	75 bp	25%	5.7
HJJT3BGX5_n01_ir64_4bs_1_1	63.2%	53%	75 bp	25%	7.7
HJJT3BGX5_n01_ir64_4bs_1_2	56.0%	52%	75 bp	33%	11.4
HJJT3BGX5_n01_ir64_4bs_6_1	77.7%	53%	75 bp	25%	10.1
HJJT3BGX5_n01_ir64_4bs_6_2	58.6%	54%	75 bp	25%	4.9
HJJT3BGX5_n01_ir64_4bs_9_1	58.6%	53%	75 bp	25%	6.7
HJJT3BGX5_n01_ir64_4bs_9_2	6.8%	53%	75 bp	8%	0.0

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

Sort	Group	Column	Description	ID	Scale
\|\|	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

Run Statistics

Showing ¹/₁ rows and ⁴/₄ columns.

Number of Lanes	Total # of Single-End Reads	Total # PF Reads	Undetermined	% PhiX Aligned
4.0	448808804	418655921	4.5	1.7

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

Sort	Column	Description	ID	Scale
\|\|	Total # of Single-End Reads	Total # of Single-End Reads	`Total # of Single-End Reads`	None
\|\|	Total # PF Reads	Total # PF Reads	`Total # PF Reads`	None
\|\|	Undetermined	Undetermined	`Undetermined`	None
\|\|	% PhiX Aligned	% PhiX Aligned	`% PhiX Aligned`	None

Demultiplexing Report

Demultiplexing Report
Total Read Count: Total number of PF (Passing Filter) reads in this library.
Portion: The proportion of reads that represent the individual library in the entire Library Pool.
Perfect: The percentage of reads in this library which have a barcode perfectly matching the barcode specified in TuboWeb. The remainder of reads have mismatches upto the max number of mismatches specified in TuboWeb (Allowed barcode mismatch option in your Library Pool).

Showing ⁴⁰/₄₀ rows and ³/₃ columns.

Library	Total Read Count	Portion (%)	Perfect (%)
ir64_3bs_12_1	16473248	4.1	100.0
ir64_3bs_6_2	8594911	2.1	100.0
ir108_4bs_9_1	6654662	1.7	100.0
ir108_3bs_6_2	8940687	2.2	100.0
ir108_4bs_6_2	9606718	2.4	100.0
ir64_4bs_12_1	25185661	6.3	100.0
ir64_3bs_9_2	8073815	2.0	100.0
ir108_4bs_6_1	12695563	3.2	100.0
ir108_3bs_1_1	9425012	2.4	100.0
ir108_4bs_1_1	6884200	1.7	100.0
ir64_3bs_6_1	10111625	2.5	100.0
ir64_4bs_6_2	4896190	1.2	100.0
ir108_4bs_1_2	5955202	1.5	100.0
ir64_4bs_1_1	7728725	1.9	100.0
ir108_4bs_12_2	15789798	3.9	100.0
ir64_4bs_11_1	15192396	3.8	100.0
ir64_3bs_1_1	16152424	4.0	100.0
ir64_4bs_11_2	8117073	2.0	100.0
ir108_3bs_9_1	6051867	1.5	100.0
ir108_3bs_12_2	3657456	0.9	100.0
ir108_3bs_9_2	11215135	2.8	100.0
ir108_4bs_11_1	10239238	2.6	100.0
ir108_3bs_1_2	6660211	1.7	100.0
ir108_4bs_12_1	7865005	2.0	100.0
ir64_4bs_6_1	10108801	2.5	100.0
ir64_3bs_12_2	12072519	3.0	100.0
ir108_3bs_11_2	9177649	2.3	100.0
ir64_4bs_12_2	5666935	1.4	100.0
ir64_3bs_1_2	6736453	1.7	100.0
ir108_4bs_11_2	6162590	1.5	100.0
ir108_3bs_6_1	13291164	3.3	100.0
ir108_3bs_11_1	15303666	3.8	100.0
ir64_3bs_9_1	8946219	2.2	100.0
ir64_4bs_1_2	11378666	2.8	100.0
ir64_3bs_11_2	6450346	1.6	100.0
ir64_4bs_9_2	4916	0.0	100.0
ir64_3bs_11_1	14502062	3.6	100.0
ir64_4bs_9_1	6670273	1.7	100.0
ir108_3bs_12_1	25092420	6.3	100.0
ir108_4bs_9_2	6185866	1.5	100.0

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

Sort	Column	Description	ID	Scale
\|\|	Total Read Count	Total Read Count	`Total Read Count`	None
\|\|	Portion (%)	Portion (%)	`Portion (%)`	None
\|\|	Perfect (%)	Perfect (%)	`Perfect (%)`	None

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 heatmap row to see a line plot for that dataset.

rollover for sample name

Position: -

%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.

40 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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General Statistics

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FastQC

Sequence Quality Histograms

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Per Sequence GC Content

Per Base N Content

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

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