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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 2018-04-06, 16:04 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HLNNLBGX5/merged

General Statistics

Showing ⁴⁸/₄₈ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
HLNNLBGX5_n01_ir108_3bs-22_1	58.9%	53%	75 bp	25%	3.7
HLNNLBGX5_n01_ir108_3bs-22_2	65.6%	53%	75 bp	25%	3.7
HLNNLBGX5_n01_ir108_3bs-25_1	74.2%	53%	75 bp	25%	10.5
HLNNLBGX5_n01_ir108_3bs-25_2	75.7%	54%	75 bp	25%	13.2
HLNNLBGX5_n01_ir108_3bs-28_1	79.3%	53%	75 bp	25%	16.6
HLNNLBGX5_n01_ir108_3bs-28_2	81.2%	54%	75 bp	25%	29.5
HLNNLBGX5_n01_ir108_3bw-22_1	72.5%	54%	75 bp	25%	7.5
HLNNLBGX5_n01_ir108_3bw-22_2	73.5%	53%	75 bp	25%	5.4
HLNNLBGX5_n01_ir108_3bw-25_1	77.4%	54%	75 bp	25%	6.9
HLNNLBGX5_n01_ir108_3bw-25_2	76.4%	54%	75 bp	25%	4.5
HLNNLBGX5_n01_ir108_3bw-28_1	83.7%	54%	75 bp	25%	12.8
HLNNLBGX5_n01_ir108_3bw-28_2	0.0%	50%	75 bp	33%	0.0
HLNNLBGX5_n01_ir108_4bs-22_1	67.0%	54%	75 bp	25%	4.3
HLNNLBGX5_n01_ir108_4bs-22_2	70.0%	54%	75 bp	25%	6.2
HLNNLBGX5_n01_ir108_4bs-25_1	77.6%	54%	75 bp	25%	11.9
HLNNLBGX5_n01_ir108_4bs-25_2	70.3%	54%	75 bp	25%	8.1
HLNNLBGX5_n01_ir108_4bs-28_1	85.8%	54%	75 bp	25%	24.4
HLNNLBGX5_n01_ir108_4bs-28_2	83.3%	54%	75 bp	25%	16.7
HLNNLBGX5_n01_ir108_4bw-22_1	68.9%	53%	75 bp	25%	6.1
HLNNLBGX5_n01_ir108_4bw-22_2	69.4%	53%	75 bp	25%	5.4
HLNNLBGX5_n01_ir108_4bw-25_1	81.8%	54%	75 bp	25%	7.8
HLNNLBGX5_n01_ir108_4bw-25_2	70.4%	53%	75 bp	25%	5.0
HLNNLBGX5_n01_ir108_4bw-28_1	82.7%	54%	75 bp	25%	9.2
HLNNLBGX5_n01_ir108_4bw-28_2	80.2%	55%	75 bp	25%	4.1
HLNNLBGX5_n01_ir64_3bs-22_1	55.5%	53%	75 bp	25%	2.3
HLNNLBGX5_n01_ir64_3bs-22_2	67.3%	54%	75 bp	25%	2.8
HLNNLBGX5_n01_ir64_3bs-25_1	70.3%	53%	75 bp	25%	6.0
HLNNLBGX5_n01_ir64_3bs-25_2	77.0%	54%	75 bp	25%	9.5
HLNNLBGX5_n01_ir64_3bs-28_1	80.8%	54%	75 bp	25%	10.2
HLNNLBGX5_n01_ir64_3bs-28_2	72.6%	53%	75 bp	25%	10.5
HLNNLBGX5_n01_ir64_3bw-22_1	79.8%	54%	75 bp	25%	15.0
HLNNLBGX5_n01_ir64_3bw-22_2	74.3%	54%	75 bp	25%	3.4
HLNNLBGX5_n01_ir64_3bw-25_1	75.4%	54%	75 bp	25%	6.5
HLNNLBGX5_n01_ir64_3bw-25_2	79.0%	54%	75 bp	25%	8.6
HLNNLBGX5_n01_ir64_3bw-28_1	80.5%	54%	75 bp	25%	7.9
HLNNLBGX5_n01_ir64_3bw-28_2	84.4%	54%	75 bp	25%	8.3
HLNNLBGX5_n01_ir64_4bs-22_1	49.1%	54%	75 bp	17%	2.3
HLNNLBGX5_n01_ir64_4bs-22_2	55.7%	53%	75 bp	25%	2.6
HLNNLBGX5_n01_ir64_4bs-25_1	70.3%	53%	75 bp	25%	10.7
HLNNLBGX5_n01_ir64_4bs-25_2	62.4%	54%	75 bp	25%	8.5
HLNNLBGX5_n01_ir64_4bs-28_1	80.3%	54%	75 bp	25%	9.7
HLNNLBGX5_n01_ir64_4bs-28_2	82.2%	53%	75 bp	25%	10.7
HLNNLBGX5_n01_ir64_4bw-22_1	73.2%	53%	75 bp	25%	3.5
HLNNLBGX5_n01_ir64_4bw-22_2	65.3%	52%	75 bp	25%	2.8
HLNNLBGX5_n01_ir64_4bw-25_1	79.6%	54%	75 bp	25%	9.2
HLNNLBGX5_n01_ir64_4bw-25_2	78.9%	54%	75 bp	25%	9.2
HLNNLBGX5_n01_ir64_4bw-28_1	84.0%	54%	75 bp	25%	12.1
HLNNLBGX5_n01_ir64_4bw-28_2	83.2%	54%	75 bp	25%	12.0

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	455588533	421888029	3.3	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 ⁴⁸/₄₈ rows and ³/₃ columns.

Library	Total Read Count	Portion (%)	Perfect (%)
ir108_3bw-25_1	6894261	1.7	100.0
ir108_3bw-28_2	43.0	0.0	100.0
ir64_4bw-22_1	3451252	0.8	100.0
ir108_4bw-25_1	7795078	1.9	100.0
ir108_3bw-22_1	7478223	1.8	100.0
ir64_4bw-25_2	9196797	2.3	100.0
ir108_3bs-25_2	13184060	3.2	100.0
ir108_4bw-28_1	9176952	2.3	100.0
ir64_3bs-25_2	9526635	2.3	100.0
ir64_4bw-22_2	2820120	0.7	100.0
ir108_3bs-25_1	10489661	2.6	100.0
ir64_3bw-25_1	6470609	1.6	100.0
ir64_3bs-22_2	2777183	0.7	100.0
ir108_3bw-28_1	12786321	3.1	100.0
ir64_3bw-28_2	8301944	2.0	100.0
ir108_4bw-28_2	4132101	1.0	100.0
ir108_3bw-25_2	4476317	1.1	100.0
ir64_3bw-22_1	15017739	3.7	100.0
ir64_3bw-28_1	7888323	1.9	100.0
ir64_4bs-25_2	8454542	2.1	100.0
ir108_3bs-22_1	3705962	0.9	100.0
ir108_4bw-22_2	5442699	1.3	100.0
ir108_3bw-22_2	5408720	1.3	100.0
ir64_4bs-25_1	10731362	2.6	100.0
ir64_3bw-22_2	3385650	0.8	100.0
ir64_4bw-25_1	9227150	2.3	100.0
ir64_3bs-28_1	10212091	2.5	100.0
ir108_4bs-25_1	11945375	2.9	100.0
ir108_4bs-22_2	6162806	1.5	100.0
ir108_4bs-25_2	8144474	2.0	100.0
ir108_3bs-22_2	3669177	0.9	100.0
ir108_4bs-28_1	24408115	6.0	100.0
ir108_3bs-28_2	29476009	7.2	100.0
ir64_3bs-28_2	10522801	2.6	100.0
ir64_4bw-28_1	12147871	3.0	100.0
ir108_4bs-22_1	4257161	1.0	100.0
ir64_4bw-28_2	11982162	2.9	100.0
ir108_4bs-28_2	16718981	4.1	100.0
ir64_4bs-22_1	2306531	0.6	100.0
ir108_4bw-22_1	6120470	1.5	100.0
ir108_4bw-25_2	5002130	1.2	100.0
ir64_4bs-28_1	9654791	2.4	100.0
ir64_3bs-22_1	2293986	0.6	100.0
ir64_3bs-25_1	6043857	1.5	100.0
ir64_3bw-25_2	8613671	2.1	100.0
ir108_3bs-28_1	16623015	4.1	100.0
ir64_4bs-22_2	2602468	0.6	100.0
ir64_4bs-28_2	10680898	2.6	100.0

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 (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.

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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Per Sequence GC Content

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Sequence Length Distribution

Sequence Duplication Levels

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