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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 2017-07-08, 09:07 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HKHNTBCXY/1

General Statistics

Showing ²²/₂₂ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
HKHNTBCXY_l01n01_h-30ar-1.35100000093fd5	75.2%	40%	51 bp	17%	13.8
HKHNTBCXY_l01n01_h-30ar-2.35100000093fff	57.2%	39%	51 bp	17%	12.9
HKHNTBCXY_l01n01_hk-120ar-1.35100000093f5f	48.6%	40%	51 bp	8%	2.5
HKHNTBCXY_l01n01_hk-120ar-2.35100000093fc8	64.4%	45%	51 bp	50%	35.7
HKHNTBCXY_l01n01_hk-30ar-1.35100000093ee3	65.6%	41%	51 bp	25%	16.8
HKHNTBCXY_l01n01_hk-30ar-2.35100000093f6b	48.8%	44%	51 bp	42%	5.5
HKHNTBCXY_l01n01_hk-60ar-1.35100000093f0e	27.2%	40%	51 bp	8%	1.8
HKHNTBCXY_l01n01_hk-60ar-2.35100000093f85	55.4%	42%	51 bp	42%	29.5
HKHNTBCXY_l01n01_hk-90ar-1.35100000093f28	49.5%	40%	51 bp	8%	3.5
HKHNTBCXY_l01n01_hk-90ar-2.35100000093faf	47.3%	48%	51 bp	33%	0.0
HKHNTBCXY_l01n01_k-30ar-1.35100000094024	59.0%	40%	51 bp	25%	14.2
HKHNTBCXY_l01n02_h-30ar-1.35200000093fd2	68.7%	42%	51 bp	25%	13.8
HKHNTBCXY_l01n02_h-30ar-2.35200000093ffc	51.5%	41%	51 bp	25%	12.9
HKHNTBCXY_l01n02_hk-120ar-1.35200000093f5c	43.1%	42%	51 bp	17%	2.5
HKHNTBCXY_l01n02_hk-120ar-2.35200000093fc5	58.9%	46%	51 bp	50%	35.7
HKHNTBCXY_l01n02_hk-30ar-1.35200000093ee0	60.5%	42%	51 bp	25%	16.8
HKHNTBCXY_l01n02_hk-30ar-2.35200000093f68	44.1%	45%	51 bp	42%	5.5
HKHNTBCXY_l01n02_hk-60ar-1.35200000093f0b	24.5%	41%	51 bp	17%	1.8
HKHNTBCXY_l01n02_hk-60ar-2.35200000093f82	51.8%	42%	51 bp	42%	29.5
HKHNTBCXY_l01n02_hk-90ar-1.35200000093f25	43.5%	42%	51 bp	17%	3.5
HKHNTBCXY_l01n02_hk-90ar-2.35200000093fac	14.3%	52%	51 bp	58%	0.0
HKHNTBCXY_l01n02_k-30ar-1.35200000094021	54.6%	41%	51 bp	25%	14.2

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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

Lane Statistics

Showing ¹/₁ rows and ³/₃ columns.

Lane	Total # of Single-End Reads	Total # PF Reads	Undetermined
1.0	191001041	178331469	23.62%

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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

Lane 1 Demultiplexing Report

Lane 1 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 ¹¹/₁₁ rows and ³/₃ columns.

Library	Total Read Count	Portion (%)	Perfect (%)
hk-90ar-2	22445	0.0	0.8
hk-30ar-2	5515982	4.0	94.8
hk-30ar-1	16776258	12.3	98.6
h-30ar-2	12938340	9.5	98.7
hk-120ar-2	35724443	26.2	97.2
hk-120ar-1	2474803	1.8	98.7
h-30ar-1	13793708	10.1	98.4
k-30ar-1	14192883	10.4	98.7
hk-90ar-1	3516174	2.6	98.5
hk-60ar-1	1804389	1.3	98.4
hk-60ar-2	29453273	21.6	97.6

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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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%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 (51bp).

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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About MultiQC

General Statistics

General Statistics: Columns

Lane Statistics

Table Ekwg: Columns

Lane 1 Demultiplexing Report

Table Nqlv: 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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