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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 2017-07-24, 17:07 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HMN35AFXX/merged

General Statistics

Showing ⁵⁸/₅₈ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
HMN35AFXX_n01_mah137	23.8%	41%	150 bp	25%	2.5
HMN35AFXX_n01_mah148	27.6%	41%	150 bp	25%	3.2
HMN35AFXX_n01_mah33	27.3%	42%	150 bp	25%	3.1
HMN35AFXX_n01_mah4	28.4%	42%	150 bp	25%	3.5
HMN35AFXX_n01_mah58	31.0%	41%	150 bp	25%	3.4
HMN35AFXX_n01_mas4x58p110b	46.9%	41%	150 bp	25%	7.6
HMN35AFXX_n01_mas4x58p111d	40.0%	41%	150 bp	25%	6.4
HMN35AFXX_n01_mas4x58p112c	30.9%	41%	150 bp	25%	3.2
HMN35AFXX_n01_mas4x58p11d	26.6%	43%	150 bp	25%	3.1
HMN35AFXX_n01_mas4x58p12f	31.3%	42%	150 bp	25%	3.3
HMN35AFXX_n01_mas4x58p13d	49.0%	41%	150 bp	25%	10.2
HMN35AFXX_n01_mas4x58p13g	28.5%	41%	150 bp	25%	2.7
HMN35AFXX_n01_mas4x58p14h	29.7%	40%	150 bp	25%	2.9
HMN35AFXX_n01_mas4x58p15g	27.6%	41%	150 bp	25%	2.9
HMN35AFXX_n01_mas4x58p17c	33.4%	40%	150 bp	25%	3.5
HMN35AFXX_n01_mas4x58p17h	33.9%	40%	150 bp	25%	3.8
HMN35AFXX_n01_mas4x58p18e	32.5%	42%	150 bp	25%	4.0
HMN35AFXX_n01_mas4x58p210c	28.6%	41%	150 bp	25%	2.1
HMN35AFXX_n01_mas4x58p212g	32.1%	41%	150 bp	25%	3.5
HMN35AFXX_n01_mas4x58p21b	34.8%	42%	150 bp	25%	4.3
HMN35AFXX_n01_mas4x58p22e	33.1%	41%	150 bp	25%	4.0
HMN35AFXX_n01_mas4x58p23c	28.7%	41%	150 bp	25%	2.8
HMN35AFXX_n01_mas4x58p25e	30.3%	42%	150 bp	25%	2.9
HMN35AFXX_n01_mas4x58p27g	35.4%	42%	150 bp	25%	4.6
HMN35AFXX_n01_mas4x58p28c	34.8%	41%	150 bp	25%	4.6
HMN35AFXX_n01_mata1	31.6%	41%	150 bp	25%	3.5
HMN35AFXX_n01_mata2	35.7%	41%	150 bp	25%	4.7
HMN35AFXX_n01_matalpha1	33.8%	41%	150 bp	25%	4.3
HMN35AFXX_n01_matalpha2	44.7%	40%	150 bp	25%	7.5
HMN35AFXX_n02_mah137	22.7%	41%	150 bp	25%	2.5
HMN35AFXX_n02_mah148	26.9%	41%	150 bp	25%	3.2
HMN35AFXX_n02_mah33	26.7%	41%	150 bp	25%	3.1
HMN35AFXX_n02_mah4	27.6%	41%	150 bp	25%	3.5
HMN35AFXX_n02_mah58	29.8%	41%	150 bp	25%	3.4
HMN35AFXX_n02_mas4x58p110b	46.5%	41%	150 bp	25%	7.6
HMN35AFXX_n02_mas4x58p111d	39.0%	40%	150 bp	25%	6.4
HMN35AFXX_n02_mas4x58p112c	30.0%	40%	150 bp	25%	3.2
HMN35AFXX_n02_mas4x58p11d	26.0%	42%	150 bp	25%	3.1
HMN35AFXX_n02_mas4x58p12f	31.2%	41%	150 bp	25%	3.3
HMN35AFXX_n02_mas4x58p13d	46.8%	41%	150 bp	25%	10.2
HMN35AFXX_n02_mas4x58p13g	27.5%	40%	150 bp	25%	2.7
HMN35AFXX_n02_mas4x58p14h	28.9%	40%	150 bp	25%	2.9
HMN35AFXX_n02_mas4x58p15g	26.4%	40%	150 bp	25%	2.9
HMN35AFXX_n02_mas4x58p17c	32.0%	40%	150 bp	25%	3.5
HMN35AFXX_n02_mas4x58p17h	31.7%	40%	150 bp	17%	3.8
HMN35AFXX_n02_mas4x58p18e	32.0%	41%	150 bp	25%	4.0
HMN35AFXX_n02_mas4x58p210c	27.0%	40%	150 bp	25%	2.1
HMN35AFXX_n02_mas4x58p212g	31.1%	41%	150 bp	25%	3.5
HMN35AFXX_n02_mas4x58p21b	34.3%	41%	150 bp	25%	4.3
HMN35AFXX_n02_mas4x58p22e	31.9%	41%	150 bp	25%	4.0
HMN35AFXX_n02_mas4x58p23c	28.1%	41%	150 bp	25%	2.8
HMN35AFXX_n02_mas4x58p25e	29.3%	41%	150 bp	25%	2.9
HMN35AFXX_n02_mas4x58p27g	34.1%	41%	150 bp	25%	4.6
HMN35AFXX_n02_mas4x58p28c	34.5%	41%	150 bp	25%	4.6
HMN35AFXX_n02_mata1	30.7%	41%	150 bp	25%	3.5
HMN35AFXX_n02_mata2	35.0%	40%	150 bp	25%	4.7
HMN35AFXX_n02_matalpha1	33.4%	40%	150 bp	25%	4.3
HMN35AFXX_n02_matalpha2	43.0%	40%	150 bp	25%	7.5

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 ³/₃ columns.

Number of Lanes	Total # of Single-End Reads	Total # PF Reads	Undetermined
4.0	131568780	124098407	1.17%

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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

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 ²⁹/₂₉ rows and ³/₃ columns.

Library	Total Read Count	Portion (%)	Perfect (%)
mas4x58p13g	2720952	2.3	97.1
mata1	3470780	2.9	97.9
mas4x58p28c	4622844	3.9	97.2
mah58	3408567	2.9	97.7
matalpha1	4290050	3.6	98.0
mas4x58p18e	4015086	3.4	97.8
mata2	4671619	4.0	95.2
mas4x58p110b	7572942	6.4	97.7
mah33	3125315	2.6	97.5
mas4x58p15g	2931497	2.5	95.8
mas4x58p212g	3459353	2.9	97.5
mas4x58p17c	3488574	3.0	97.7
mah137	2544403	2.2	97.2
mas4x58p17h	3776884	3.2	97.8
mas4x58p21b	4324361	3.7	97.4
mas4x58p27g	4582050	3.9	97.4
mas4x58p112c	3235958	2.7	97.4
mas4x58p14h	2922264	2.5	97.5
mas4x58p11d	3126067	2.6	97.2
mas4x58p13d	10152521	8.6	97.6
mah148	3237213	2.7	97.6
mas4x58p22e	4002460	3.4	97.2
mas4x58p25e	2910599	2.5	96.8
matalpha2	7529185	6.4	98.0
mas4x58p111d	6386017	5.4	97.9
mas4x58p12f	3344006	2.8	97.2
mas4x58p210c	2125713	1.8	97.6
mah4	3453253	2.9	97.4
mas4x58p23c	2763799	2.3	97.5

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 (150bp).

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.

58 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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FastQC

Sequence Quality Histograms

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Per Sequence GC Content

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Sequence Length Distribution

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

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