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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 2018-01-12, 16:01 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HMYHGBBXX/4

General Statistics

Showing ²⁶/₂₆ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
HMYHGBBXX_l04n01_dj03.351000000b72e0	97.7%	37%	76 bp	42%	8.9
HMYHGBBXX_l04n01_dj04.351000000b7318	94.2%	41%	76 bp	42%	40.6
HMYHGBBXX_l04n01_dj05.351000000b7332	96.1%	38%	76 bp	42%	14.0
HMYHGBBXX_l04n01_dj07.351000000b7368	95.7%	42%	76 bp	42%	32.3
HMYHGBBXX_l04n01_las54.351000000b711a	38.3%	38%	76 bp	33%	28.8
HMYHGBBXX_l04n01_las55.351000000b715e	29.8%	37%	76 bp	17%	30.2
HMYHGBBXX_l04n01_las56.351000000b7184	20.2%	37%	76 bp	17%	25.2
HMYHGBBXX_l04n01_las59.351000000b71ba	20.1%	38%	76 bp	17%	36.8
HMYHGBBXX_l04n01_las60.351000000b71e1	18.2%	38%	76 bp	17%	27.6
HMYHGBBXX_l04n01_las61.351000000b7226	16.7%	38%	76 bp	17%	22.5
HMYHGBBXX_l04n01_las62.351000000b725d	22.6%	39%	76 bp	33%	14.0
HMYHGBBXX_l04n01_las65.351000000b7283	97.3%	43%	76 bp	42%	35.1
HMYHGBBXX_l04n01_las70.351000000b72b9	16.2%	38%	76 bp	17%	19.2
HMYHGBBXX_l04n02_dj03.352000000b72ed	85.4%	37%	76 bp	58%	8.9
HMYHGBBXX_l04n02_dj04.352000000b7315	96.1%	42%	76 bp	42%	40.6
HMYHGBBXX_l04n02_dj05.352000000b733f	93.3%	30%	76 bp	42%	14.0
HMYHGBBXX_l04n02_dj07.352000000b7365	97.3%	42%	76 bp	33%	32.3
HMYHGBBXX_l04n02_las54.352000000b7117	36.9%	38%	76 bp	25%	28.8
HMYHGBBXX_l04n02_las55.352000000b715b	27.7%	37%	76 bp	17%	30.2
HMYHGBBXX_l04n02_las56.352000000b7181	18.7%	37%	76 bp	17%	25.2
HMYHGBBXX_l04n02_las59.352000000b71b7	19.5%	37%	76 bp	17%	36.8
HMYHGBBXX_l04n02_las60.352000000b71ee	17.4%	37%	76 bp	17%	27.6
HMYHGBBXX_l04n02_las61.352000000b7223	15.8%	38%	76 bp	17%	22.5
HMYHGBBXX_l04n02_las62.352000000b725a	20.7%	38%	76 bp	25%	14.0
HMYHGBBXX_l04n02_las65.352000000b7280	96.2%	43%	76 bp	50%	35.1
HMYHGBBXX_l04n02_las70.352000000b72b6	15.7%	38%	76 bp	17%	19.2

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
4.0	482988240	340469762	1.6	0.0

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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 4 Demultiplexing Report

Lane 4 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 ¹³/₁₃ rows and ³/₃ columns.

Library	Total Read Count	Portion (%)	Perfect (%)
las54	28769858	8.6	98.0
las62	13956272	4.2	98.3
dj05	13967111	4.2	98.1
las65	35084358	10.5	97.8
las61	22530091	6.7	98.4
dj03	8893992	2.7	97.8
dj07	32315749	9.6	97.2
las56	25168232	7.5	98.2
las70	19186951	5.7	96.3
dj04	40627747	12.1	97.3
las59	36772981	11.0	97.5
las55	30237542	9.0	98.1
las60	27576294	8.2	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 (76bp).

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

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Lane 4 Demultiplexing Report

Table Sdub: 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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