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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 2018-05-22, 20:05 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVKKNBGX5/merged

General Statistics

Showing ⁶⁴/₆₄ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
HVKKNBGX5_n01_a10	28.1%	44%	75 bp	33%	6.7
HVKKNBGX5_n01_a6	30.8%	45%	75 bp	33%	21.5
HVKKNBGX5_n01_a9	38.6%	45%	75 bp	25%	39.2
HVKKNBGX5_n01_b10	27.9%	45%	75 bp	25%	9.7
HVKKNBGX5_n01_b11	28.9%	45%	75 bp	33%	11.4
HVKKNBGX5_n01_b4	22.8%	46%	75 bp	25%	8.9
HVKKNBGX5_n01_c1	21.8%	46%	75 bp	25%	10.9
HVKKNBGX5_n01_c10	38.6%	45%	75 bp	25%	32.5
HVKKNBGX5_n01_c11	27.2%	46%	75 bp	25%	11.2
HVKKNBGX5_n01_c2	89.0%	47%	75 bp	33%	4.3
HVKKNBGX5_n01_c4	37.1%	46%	75 bp	25%	51.8
HVKKNBGX5_n01_d2	18.2%	47%	75 bp	25%	9.6
HVKKNBGX5_n01_e1	22.8%	46%	75 bp	25%	10.0
HVKKNBGX5_n01_e11	25.1%	46%	75 bp	25%	10.4
HVKKNBGX5_n01_e12	16.7%	47%	75 bp	25%	7.7
HVKKNBGX5_n01_e4	24.4%	46%	75 bp	25%	9.9
HVKKNBGX5_n01_e6	21.0%	46%	75 bp	25%	10.4
HVKKNBGX5_n01_f11	26.6%	45%	75 bp	25%	7.3
HVKKNBGX5_n01_f8	26.1%	45%	75 bp	25%	6.7
HVKKNBGX5_n01_g10	13.0%	47%	75 bp	25%	2.2
HVKKNBGX5_n01_g11	15.7%	47%	75 bp	25%	7.2
HVKKNBGX5_n01_g2	25.3%	45%	75 bp	25%	6.7
HVKKNBGX5_n01_g4	22.9%	45%	75 bp	25%	5.5
HVKKNBGX5_n01_g5	17.4%	45%	75 bp	25%	5.0
HVKKNBGX5_n01_g6	33.0%	44%	75 bp	33%	10.5
HVKKNBGX5_n01_g9	34.8%	44%	75 bp	25%	12.8
HVKKNBGX5_n01_h1	21.6%	45%	75 bp	25%	4.7
HVKKNBGX5_n01_h4	24.4%	45%	75 bp	25%	5.9
HVKKNBGX5_n01_h6	11.0%	46%	75 bp	25%	6.6
HVKKNBGX5_n01_h7	32.3%	43%	75 bp	33%	5.7
HVKKNBGX5_n01_h8	24.3%	45%	75 bp	25%	6.1
HVKKNBGX5_n01_h9	22.5%	46%	75 bp	25%	9.9
HVKKNBGX5_n02_a10	28.0%	44%	75 bp	33%	6.7
HVKKNBGX5_n02_a6	30.1%	45%	75 bp	33%	21.5
HVKKNBGX5_n02_a9	37.8%	45%	75 bp	33%	39.2
HVKKNBGX5_n02_b10	27.8%	45%	75 bp	33%	9.7
HVKKNBGX5_n02_b11	28.4%	44%	75 bp	33%	11.4
HVKKNBGX5_n02_b4	22.5%	45%	75 bp	25%	8.9
HVKKNBGX5_n02_c1	21.6%	46%	75 bp	25%	10.9
HVKKNBGX5_n02_c10	37.9%	45%	75 bp	33%	32.5
HVKKNBGX5_n02_c11	27.0%	45%	75 bp	25%	11.2
HVKKNBGX5_n02_c2	87.7%	47%	75 bp	33%	4.3
HVKKNBGX5_n02_c4	35.9%	46%	75 bp	25%	51.8
HVKKNBGX5_n02_d2	17.8%	47%	75 bp	25%	9.6
HVKKNBGX5_n02_e1	22.2%	46%	75 bp	33%	10.0
HVKKNBGX5_n02_e11	24.6%	46%	75 bp	25%	10.4
HVKKNBGX5_n02_e12	16.5%	46%	75 bp	25%	7.7
HVKKNBGX5_n02_e4	24.0%	46%	75 bp	25%	9.9
HVKKNBGX5_n02_e6	21.0%	46%	75 bp	25%	10.4
HVKKNBGX5_n02_f11	26.6%	45%	75 bp	33%	7.3
HVKKNBGX5_n02_f8	25.4%	45%	75 bp	25%	6.7
HVKKNBGX5_n02_g10	13.2%	46%	75 bp	33%	2.2
HVKKNBGX5_n02_g11	15.5%	47%	75 bp	25%	7.2
HVKKNBGX5_n02_g2	24.3%	45%	75 bp	25%	6.7
HVKKNBGX5_n02_g4	22.6%	45%	75 bp	25%	5.5
HVKKNBGX5_n02_g5	16.8%	45%	75 bp	25%	5.0
HVKKNBGX5_n02_g6	32.1%	44%	75 bp	33%	10.5
HVKKNBGX5_n02_g9	34.4%	44%	75 bp	33%	12.8
HVKKNBGX5_n02_h1	20.9%	45%	75 bp	25%	4.7
HVKKNBGX5_n02_h4	23.7%	45%	75 bp	25%	5.9
HVKKNBGX5_n02_h6	10.8%	46%	75 bp	25%	6.6
HVKKNBGX5_n02_h7	31.7%	43%	75 bp	33%	5.7
HVKKNBGX5_n02_h8	23.9%	45%	75 bp	33%	6.1
HVKKNBGX5_n02_h9	21.8%	46%	75 bp	33%	9.9

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	406188390	385860405	4.4	1.6

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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 (%)
b4	8924508	2.4	98.0
g5	5039934	1.4	97.8
e6	10357842	2.8	98.1
h8	6104863	1.7	96.3
b11	11383133	3.1	98.2
e11	10360788	2.8	98.0
h6	6573863	1.8	96.2
c11	11240826	3.0	98.2
c10	32470099	8.8	98.2
c2	4339759	1.2	97.8
a6	21479709	5.8	98.1
g9	12766305	3.5	97.9
h1	4693162	1.3	96.5
e4	9928747	2.7	98.1
b10	9698177	2.6	97.8
d2	9587715	2.6	98.0
a10	6654014	1.8	98.0
h9	9898812	2.7	96.5
a9	39177250	10.6	98.2
f11	7341616	2.0	97.8
f8	6674063	1.8	98.0
h7	5655845	1.5	96.7
g4	5531960	1.5	97.9
g10	2234312	0.6	96.7
g6	10528617	2.9	98.1
g11	7236257	2.0	96.6
c1	10916555	3.0	97.9
e12	7695672	2.1	97.7
e1	10010758	2.7	98.1
c4	51847985	14.1	98.2
g2	6740180	1.8	97.8
h4	5894052	1.6	96.5

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 (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.

64 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.

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General Statistics

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Demultiplexing Report

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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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