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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 2018-01-10, 00:01 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H5JWNBCX2/2

General Statistics

Showing ²⁴/₂₄ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
H5JWNBCX2_l02n01_3002_d3.351000000b7af5	48.3%	53%	101 bp	25%	14.4
H5JWNBCX2_l02n01_3004_d8.351000000b7b60	50.3%	53%	101 bp	33%	16.8
H5JWNBCX2_l02n01_3005_d1.351000000b7ace	74.0%	57%	101 bp	42%	18.3
H5JWNBCX2_l02n01_3006_d1.351000000b7b47	77.8%	57%	101 bp	42%	17.1
H5JWNBCX2_l02n01_3006_d8.351000000b7a3b	58.8%	55%	101 bp	33%	16.0
H5JWNBCX2_l02n01_3010_d5.351000000b7ae8	46.4%	53%	101 bp	25%	13.8
H5JWNBCX2_l02n01_3011_d-2.351000000b7a11	71.1%	57%	101 bp	42%	17.0
H5JWNBCX2_l02n01_3024_d3.351000000b7b10	47.9%	53%	101 bp	25%	14.0
H5JWNBCX2_l02n01_3025_d8.351000000b7aa5	62.3%	55%	101 bp	33%	17.4
H5JWNBCX2_l02n01_3029_d3.351000000b7a8b	48.9%	53%	101 bp	25%	15.8
H5JWNBCX2_l02n01_3033_d5.351000000b7a55	51.2%	53%	101 bp	33%	14.4
H5JWNBCX2_l02n01_3036_d8.351000000b7b7d	50.9%	53%	101 bp	33%	16.4
H5JWNBCX2_l02n02_3002_d3.352000000b7af2	47.6%	53%	101 bp	25%	14.4
H5JWNBCX2_l02n02_3004_d8.352000000b7b6d	49.9%	53%	101 bp	25%	16.8
H5JWNBCX2_l02n02_3005_d1.352000000b7acb	73.3%	57%	101 bp	42%	18.3
H5JWNBCX2_l02n02_3006_d1.352000000b7b44	77.2%	57%	101 bp	42%	17.1
H5JWNBCX2_l02n02_3006_d8.352000000b7a38	58.3%	55%	101 bp	33%	16.0
H5JWNBCX2_l02n02_3010_d5.352000000b7ae5	46.3%	53%	101 bp	25%	13.8
H5JWNBCX2_l02n02_3011_d-2.352000000b7a1e	70.7%	57%	101 bp	42%	17.0
H5JWNBCX2_l02n02_3024_d3.352000000b7b1d	47.6%	53%	101 bp	25%	14.0
H5JWNBCX2_l02n02_3025_d8.352000000b7aa2	61.6%	55%	101 bp	33%	17.4
H5JWNBCX2_l02n02_3029_d3.352000000b7a88	47.8%	53%	101 bp	25%	15.8
H5JWNBCX2_l02n02_3033_d5.352000000b7a52	50.2%	53%	101 bp	33%	14.4
H5JWNBCX2_l02n02_3036_d8.352000000b7b7a	50.7%	53%	101 bp	33%	16.4

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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

Lane Statistics

Showing ¹/₁ rows and ⁴/₄ columns.

Lane	Total # of Single-End Reads	Total # PF Reads	Undetermined	% PhiX Aligned
2.0	204412974	194357675	1.6	1.2

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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

Lane 2 Demultiplexing Report

Lane 2 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 ¹²/₁₂ rows and ³/₃ columns.

Library	Total Read Count	Portion (%)	Perfect (%)
3006_d1	17103791	8.9	98.9
3033_d5	14393414	7.5	98.8
3025_d8	17363158	9.1	99.0
3002_d3	14399512	7.5	98.8
3006_d8	15996538	8.4	98.4
3010_d5	13758879	7.2	98.9
3024_d3	13956914	7.3	98.9
3005_d1	18272069	9.5	98.9
3029_d3	15847806	8.3	98.9
3036_d8	16435632	8.6	99.0
3011_d-2	17040535	8.9	99.1
3004_d8	16777936	8.8	99.1

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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 (101bp).

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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Lane Statistics

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Lane 2 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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