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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 2018-02-13, 04:02 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/CBNFWACXX/3

General Statistics

Showing ³⁰/₃₀ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
CBNFWACXX_l03n01_3004_d5.351000000be0a9	44.4%	52%	101 bp	25%	14.2
CBNFWACXX_l03n01_3007_d5.351000000be28d	53.3%	53%	101 bp	33%	16.1
CBNFWACXX_l03n01_3013_d-2.351000000be738	74.8%	56%	101 bp	33%	12.8
CBNFWACXX_l03n01_3014_d-2.351000000be6bf	77.8%	57%	101 bp	42%	13.9
CBNFWACXX_l03n01_3024_d-2.351000000be0f9	57.1%	54%	101 bp	33%	14.0
CBNFWACXX_l03n01_3026_d1.351000000be5a4	66.8%	55%	101 bp	33%	13.2
CBNFWACXX_l03n01_3026_d8.351000000be62c	60.0%	55%	101 bp	33%	12.3
CBNFWACXX_l03n01_3027_d3.351000000be42e	46.0%	52%	101 bp	25%	13.6
CBNFWACXX_l03n01_3027_d5.351000000be1f8	45.6%	52%	101 bp	25%	15.0
CBNFWACXX_l03n01_3028_d3.351000000be33c	47.3%	52%	101 bp	25%	12.9
CBNFWACXX_l03n01_3029_d-2.351000000be3b2	73.5%	56%	101 bp	42%	13.5
CBNFWACXX_l03n01_3029_d8.351000000be059	71.3%	56%	101 bp	42%	14.2
CBNFWACXX_l03n01_3032_d8.351000000be4a5	47.9%	53%	101 bp	25%	14.2
CBNFWACXX_l03n01_3034_d1.351000000be52d	59.3%	54%	101 bp	33%	14.0
CBNFWACXX_l03n01_3036_d-2.351000000be171	70.5%	56%	101 bp	42%	14.2
CBNFWACXX_l03n02_3004_d5.352000000be0a6	43.9%	52%	101 bp	33%	14.2
CBNFWACXX_l03n02_3007_d5.352000000be28a	52.8%	53%	101 bp	42%	16.1
CBNFWACXX_l03n02_3013_d-2.352000000be735	73.2%	56%	101 bp	42%	12.8
CBNFWACXX_l03n02_3014_d-2.352000000be6bc	76.5%	57%	101 bp	50%	13.9
CBNFWACXX_l03n02_3024_d-2.352000000be0f6	56.2%	54%	101 bp	42%	14.0
CBNFWACXX_l03n02_3026_d1.352000000be5a1	65.3%	55%	101 bp	42%	13.2
CBNFWACXX_l03n02_3026_d8.352000000be629	58.9%	55%	101 bp	42%	12.3
CBNFWACXX_l03n02_3027_d3.352000000be42b	45.4%	52%	101 bp	33%	13.6
CBNFWACXX_l03n02_3027_d5.352000000be1f5	44.2%	52%	101 bp	33%	15.0
CBNFWACXX_l03n02_3028_d3.352000000be339	46.0%	52%	101 bp	33%	12.9
CBNFWACXX_l03n02_3029_d-2.352000000be3bf	71.2%	56%	101 bp	50%	13.5
CBNFWACXX_l03n02_3029_d8.352000000be056	70.2%	56%	101 bp	42%	14.2
CBNFWACXX_l03n02_3032_d8.352000000be4a2	47.0%	53%	101 bp	33%	14.2
CBNFWACXX_l03n02_3034_d1.352000000be52a	58.2%	54%	101 bp	42%	14.0
CBNFWACXX_l03n02_3036_d-2.352000000be17e	69.7%	56%	101 bp	42%	14.2

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

Lane Statistics

Showing ¹/₁ rows and ⁴/₄ columns.

Lane	Total # of Single-End Reads	Total # PF Reads	Undetermined	% PhiX Aligned
3.0	221986262	212889803	2.3	1.3

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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 3 Demultiplexing Report

Lane 3 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 ¹⁵/₁₅ rows and ³/₃ columns.

Library	Total Read Count	Portion (%)	Perfect (%)
3027_d5	15017386	7.2	97.8
3026_d8	12288631	5.9	98.5
3014_d-2	13880718	6.7	98.4
3029_d-2	13535180	6.5	98.2
3028_d3	12923628	6.2	98.7
3026_d1	13169666	6.3	98.4
3013_d-2	12827109	6.2	98.7
3034_d1	13982324	6.7	98.6
3036_d-2	14180140	6.8	98.2
3029_d8	14177985	6.8	98.6
3004_d5	14240949	6.8	98.4
3027_d3	13566120	6.5	98.5
3007_d5	16071930	7.7	98.1
3024_d-2	13961711	6.7	98.4
3032_d8	14249132	6.8	98.8

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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.

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 (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

General Statistics: Columns

Lane Statistics

Table Fwln: Columns

Lane 3 Demultiplexing Report

Table Jlbf: Columns

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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