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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 2018-07-13, 16:07 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H3TN2AFXY/merged

General Statistics

Showing ⁴⁶/₄₆ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
H3TN2AFXY_n01_ah6978a-0718	26.8%	39%	51 bp	8%	7.8
H3TN2AFXY_n01_ah6978i-0718	23.4%	38%	51 bp	8%	4.9
H3TN2AFXY_n01_ah7797a-0718	28.0%	39%	51 bp	8%	9.0
H3TN2AFXY_n01_ah7797i-0718	40.9%	39%	51 bp	8%	15.5
H3TN2AFXY_n01_ah7797j-0718	18.8%	39%	51 bp	8%	4.2
H3TN2AFXY_n01_ah7797k-0718	37.3%	39%	51 bp	8%	17.4
H3TN2AFXY_n01_ah8038a-0718	31.0%	39%	51 bp	8%	11.7
H3TN2AFXY_n01_ah8038i-0718	41.7%	40%	51 bp	17%	6.0
H3TN2AFXY_n01_ah8643a1-0718	26.0%	39%	51 bp	8%	9.0
H3TN2AFXY_n01_ah8643a2-0718	26.6%	40%	51 bp	8%	9.1
H3TN2AFXY_n01_ah8643i1-0718	27.5%	38%	51 bp	8%	7.8
H3TN2AFXY_n01_ah8643i2-0718	29.0%	38%	51 bp	8%	5.6
H3TN2AFXY_n01_ah9041a-0718	3.5%	39%	51 bp	0%	0.0
H3TN2AFXY_n01_ah9041i-0718	41.9%	39%	51 bp	17%	15.2
H3TN2AFXY_n01_ah9722a-0718	26.5%	39%	51 bp	8%	7.8
H3TN2AFXY_n01_ah9722b-0718	26.2%	39%	51 bp	8%	7.8
H3TN2AFXY_n01_ah9722i-0718	41.6%	40%	51 bp	8%	7.4
H3TN2AFXY_n01_ah9723a-0718	24.0%	39%	51 bp	17%	6.2
H3TN2AFXY_n01_ah9723i-0718	29.2%	38%	51 bp	8%	5.4
H3TN2AFXY_n01_ah9724a-0718	26.6%	39%	51 bp	8%	7.8
H3TN2AFXY_n01_ah9724a1-0718	24.3%	39%	51 bp	8%	6.7
H3TN2AFXY_n01_ah9724i-0718	33.6%	39%	51 bp	8%	5.9
H3TN2AFXY_n01_ah9724i1-0718	31.9%	39%	51 bp	8%	7.2
H3TN2AFXY_n02_ah6978a-0718	25.2%	39%	51 bp	8%	7.8
H3TN2AFXY_n02_ah6978i-0718	21.8%	38%	51 bp	8%	4.9
H3TN2AFXY_n02_ah7797a-0718	26.1%	39%	51 bp	17%	9.0
H3TN2AFXY_n02_ah7797i-0718	38.3%	39%	51 bp	8%	15.5
H3TN2AFXY_n02_ah7797j-0718	17.6%	39%	51 bp	0%	4.2
H3TN2AFXY_n02_ah7797k-0718	33.0%	39%	51 bp	0%	17.4
H3TN2AFXY_n02_ah8038a-0718	29.6%	39%	51 bp	0%	11.7
H3TN2AFXY_n02_ah8038i-0718	38.5%	40%	51 bp	8%	6.0
H3TN2AFXY_n02_ah8643a1-0718	24.9%	39%	51 bp	0%	9.0
H3TN2AFXY_n02_ah8643a2-0718	25.2%	41%	51 bp	25%	9.1
H3TN2AFXY_n02_ah8643i1-0718	24.9%	39%	51 bp	17%	7.8
H3TN2AFXY_n02_ah8643i2-0718	26.0%	40%	51 bp	17%	5.6
H3TN2AFXY_n02_ah9041a-0718	4.0%	41%	51 bp	17%	0.0
H3TN2AFXY_n02_ah9041i-0718	37.8%	40%	51 bp	17%	15.2
H3TN2AFXY_n02_ah9722a-0718	25.3%	39%	51 bp	8%	7.8
H3TN2AFXY_n02_ah9722b-0718	24.7%	39%	51 bp	8%	7.8
H3TN2AFXY_n02_ah9722i-0718	39.5%	40%	51 bp	8%	7.4
H3TN2AFXY_n02_ah9723a-0718	22.7%	39%	51 bp	17%	6.2
H3TN2AFXY_n02_ah9723i-0718	27.4%	38%	51 bp	8%	5.4
H3TN2AFXY_n02_ah9724a-0718	25.2%	39%	51 bp	8%	7.8
H3TN2AFXY_n02_ah9724a1-0718	22.8%	39%	51 bp	8%	6.7
H3TN2AFXY_n02_ah9724i-0718	31.4%	39%	51 bp	8%	5.9
H3TN2AFXY_n02_ah9724i1-0718	29.4%	39%	51 bp	8%	7.2

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	219897043	191115720	3.0	1.1

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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 ²³/₂₃ rows and ³/₃ columns.

Library	Total Read Count	Portion (%)	Perfect (%)
ah7797a-0718	8973310	4.8	97.9
ah6978i-0718	4896302	2.6	98.3
ah8038i-0718	6000568	3.2	96.3
ah8643i1-0718	7818844	4.2	97.8
ah7797j-0718	4189998	2.3	98.2
ah9724i-0718	5852894	3.2	98.3
ah9722b-0718	7754210	4.2	98.3
ah8038a-0718	11704144	6.3	98.3
ah6978a-0718	7778934	4.2	97.3
ah9041a-0718	17341	0.0	83.5
ah9723a-0718	6209181	3.3	98.5
ah8643a1-0718	8980173	4.8	98.4
ah8643a2-0718	9098094	4.9	98.0
ah9041i-0718	15215308	8.2	98.3
ah9724a1-0718	6723280	3.6	98.1
ah9722i-0718	7442369	4.0	98.4
ah9724a-0718	7803444	4.2	98.5
ah9724i1-0718	7225446	3.9	98.3
ah9723i-0718	5427676	2.9	98.4
ah9722a-0718	7827782	4.2	97.2
ah7797i-0718	15485623	8.4	98.1
ah8643i2-0718	5567962	3.0	98.2
ah7797k-0718	17395710	9.4	98.1

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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.

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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 (51bp).

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.

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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Demultiplexing Report

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FastQC

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

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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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