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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 2018-03-12, 21:03 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HC22WBGX5/merged

General Statistics

Showing ³²/₃₂ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
HC22WBGX5_n01_a0_1	43.6%	45%	75 bp	17%	10.8
HC22WBGX5_n01_a0_2	40.4%	45%	75 bp	17%	9.3
HC22WBGX5_n01_a0_3	43.9%	45%	75 bp	17%	11.6
HC22WBGX5_n01_a1_1	47.7%	45%	75 bp	17%	8.2
HC22WBGX5_n01_a1_2	43.9%	45%	75 bp	17%	10.4
HC22WBGX5_n01_a1_3	45.7%	46%	75 bp	17%	11.1
HC22WBGX5_n01_a2_1	44.5%	45%	75 bp	17%	13.7
HC22WBGX5_n01_a2_2	52.0%	45%	75 bp	25%	19.3
HC22WBGX5_n01_a2_3	45.9%	45%	75 bp	17%	12.9
HC22WBGX5_n01_a3_1	44.5%	45%	75 bp	17%	12.0
HC22WBGX5_n01_a3_2	48.3%	45%	75 bp	17%	15.0
HC22WBGX5_n01_a3_3	46.7%	45%	75 bp	17%	13.1
HC22WBGX5_n01_a4_1	49.5%	45%	75 bp	17%	14.3
HC22WBGX5_n01_a4_2	48.5%	45%	75 bp	17%	15.1
HC22WBGX5_n01_a4_3	49.0%	45%	75 bp	17%	15.9
HC22WBGX5_n01_a5_1	51.2%	45%	75 bp	25%	19.3
HC22WBGX5_n01_a5_2	46.4%	45%	75 bp	17%	13.4
HC22WBGX5_n01_a5_3	42.2%	45%	75 bp	17%	9.1
HC22WBGX5_n01_a6_1	44.9%	45%	75 bp	17%	11.4
HC22WBGX5_n01_a6_2	46.8%	45%	75 bp	17%	10.2
HC22WBGX5_n01_a6_3	48.4%	46%	75 bp	17%	12.1
HC22WBGX5_n01_b0_1	45.6%	45%	75 bp	17%	11.0
HC22WBGX5_n01_b0_2	54.3%	45%	75 bp	25%	23.1
HC22WBGX5_n01_b0_3	45.7%	44%	75 bp	17%	19.7
HC22WBGX5_n01_b1_1	46.8%	45%	75 bp	17%	14.2
HC22WBGX5_n01_b1_2	44.6%	45%	75 bp	17%	11.9
HC22WBGX5_n01_b1_3	50.7%	45%	75 bp	25%	18.1
HC22WBGX5_n01_b2_1	43.4%	45%	75 bp	17%	10.4
HC22WBGX5_n01_b2_2	49.5%	46%	75 bp	17%	12.6
HC22WBGX5_n01_b2_3	49.2%	45%	75 bp	17%	13.4
HC22WBGX5_n01_b3_1	54.1%	46%	75 bp	25%	16.7
HC22WBGX5_n01_b3_2	49.1%	45%	75 bp	17%	15.2

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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

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	481960167	451682909	3.8	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 ³²/₃₂ rows and ³/₃ columns.

Library	Total Read Count	Portion (%)	Perfect (%)
a2_2	19284422	4.4	100.0
a6_3	12104942	2.8	100.0
b1_2	11937425	2.7	100.0
a1_1	8241525	1.9	100.0
b3_1	16711367	3.8	100.0
b1_1	14159385	3.3	100.0
a5_2	13435288	3.1	100.0
b3_2	15205977	3.5	100.0
b0_3	19670752	4.5	100.0
b0_1	11040773	2.5	100.0
a5_3	9087291	2.1	100.0
a4_2	15055007	3.5	100.0
b2_2	12649536	2.9	100.0
a1_3	11058414	2.5	100.0
a4_1	14272459	3.3	100.0
a0_2	9281608	2.1	100.0
a5_1	19319755	4.4	100.0
a3_3	13118757	3.0	100.0
a1_2	10365029	2.4	100.0
a6_1	11392266	2.6	100.0
a0_1	10799350	2.5	100.0
b1_3	18116986	4.2	100.0
b2_1	10383074	2.4	100.0
a6_2	10246159	2.4	100.0
a2_1	13734111	3.2	100.0
a3_1	11973307	2.8	100.0
a2_3	12929949	3.0	100.0
a3_2	15034728	3.5	100.0
a4_3	15889010	3.7	100.0
b2_3	13370645	3.1	100.0
a0_3	11641210	2.7	100.0
b0_2	23073213	5.3	100.0

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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 (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.

32 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.

No samples found with any adapter contamination > 0.1%

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About MultiQC

General Statistics

General Statistics: Columns

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Demultiplexing Report

Table Oqwn: 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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