MultiQC Report

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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.

Report generated on 2020-12-05, 07:12 based on data in: /beegfs/mk5636/logs/html/H7KKVBGXH/merged

General Statistics

Showing 514 samples.

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.

Showing ²⁵⁷/₂₅₇ rows and ²/₂ columns.

Sample Name	Total Read Count	Portion (%)
undetermined_library	16,447,421	3.4
S5_R1_A01_FD	2,363,078	0.5
S5_R1_B01_FD	2,046,171	0.4
S5_R1_C01_FD	369,777	0.1
S5_R1_D01_FD	912,188	0.2
S5_R1_E01_FD	1,311,496	0.3
S5_R1_F01_FD	1,090,897	0.2
S5_R1_G01_FD	1,485,582	0.3
S5_R1_H01_FD	1,068,507	0.2
S5_R1_A02_FD	1,789,910	0.4
S5_R1_B02_FD	890,579	0.2
S5_R1_C02_FD	569,327	0.1
S5_R1_D02_FD	1,060,817	0.2
S5_R1_E02_FD	1,037,312	0.2
S5_R1_F02_FD	2,046,643	0.4
S5_R1_G02_FD	1,910,518	0.4
S5_R1_H02_FD	921,692	0.2
S5_R1_A03_FD	1,213,935	0.3
S5_R1_B03_FD	1,489,472	0.3
S5_R1_C03_FD	264,037	0.1
S5_R1_D03_FD	588,711	0.1
S5_R1_E03_FD	1,651,416	0.3
S5_R1_F03_FD	492,411	0.1
S5_R1_G03_FD	2,394,647	0.5
S5_R1_H03_FD	1,640,026	0.3
S5_R1_A04_FD	2,968,319	0.6
S5_R1_B04_FD	127,919	0.0
S5_R1_C04_FD	761,829	0.2
S5_R1_D04_FD	3,023,002	0.6
S5_R1_E04_FD	216,991	0.0
S5_R1_F04_FD	2,619,232	0.5
S5_R1_G04_FD	1,020,178	0.2
S5_R1_H04_FD	1,044,174	0.2
S5_R1_A05_FD	2,194,536	0.5
S5_R1_B05_FD	1,975,858	0.4
S5_R1_C05_FD	808,066	0.2
S5_R1_D05_FD	3,457,629	0.7
S5_R1_E05_FD	1,005,270	0.2
S5_R1_F05_FD	2,667,535	0.6
S5_R1_G05_FD	2,712,555	0.6
S5_R1_H05_FD	1,307,935	0.3
S5_R1_A06_FD	1,862,246	0.4
S5_R1_B06_FD	661,613	0.1
S5_R1_C06_FD	854,510	0.2
S5_R1_D06_FD	867,932	0.2
S5_R1_E06_FD	1,786,480	0.4
S5_R1_F06_FD	697,859	0.1
S5_R1_G06_FD	881,952	0.2
S5_R1_H06_FD	1,436,093	0.3
S5_R1_A07_FD	2,383,466	0.5
S5_R1_B07_FD	909,931	0.2
S5_R1_C07_FD	660,489	0.1
S5_R1_D07_FD	951,384	0.2
S5_R1_E07_FD	1,905,517	0.4
S5_R1_F07_FD	1,055,511	0.2
S5_R1_G07_FD	1,341,789	0.3
S5_R1_H07_FD	1,389,747	0.3
S5_R1_A08_FD	2,074,571	0.4
S5_R1_B08_FD	772,083	0.2
S5_R1_C08_FD	705,330	0.1
S5_R1_D08_FD	845,131	0.2
S5_R1_E08_FD	1,196,639	0.2
S5_R1_F08_FD	1,066,178	0.2
S5_R1_G08_FD	2,184,113	0.5
S5_R1_H08_FD	949,682	0.2
S5_R1_A09_FD	2,558,529	0.5
S5_R1_B09_FD	635,841	0.1
S5_R1_C09_FD	37,224	0.0
S5_R1_D09_FD	1,311,955	0.3
S5_R1_E09_FD	1,347,057	0.3
S5_R1_F09_FD	1,119,119	0.2
S5_R1_G09_FD	2,091,058	0.4
S5_R1_H09_FD	1,007,185	0.2
S5_R1_A10_FD	1,200,061	0.2
S5_R1_B10_FD	1,630,910	0.3
S5_R1_C10_FD	577,702	0.1
S5_R1_D10_FD	1,219,976	0.3
S5_R1_E10_FD	1,228,892	0.3
S5_R1_F10_FD	645,135	0.1
S5_R1_G10_FD	1,080,623	0.2
S5_R1_H10_FD	882,024	0.2
S5_R1_A11_FD	650,888	0.1
S5_R1_B11_FD	663,133	0.1
S5_R1_C11_FD	1,027,992	0.2
S5_R1_D11_FD	1,008,407	0.2
S5_R1_E11_FD	693,740	0.1
S5_R1_F11_FD	1,084,846	0.2
S5_R1_G11_FD	1,089,615	0.2
S5_R1_H11_FD	871,631	0.2
S5_R1_A12_FD	1,832,361	0.4
S5_R1_B12_FD	679,522	0.1
S5_R1_C12_FD	1,301,676	0.3
S5_R1_D12_FD	1,451,817	0.3
S5_R1_E12_FD	833,587	0.2
S5_R1_F12_FD	1,080,445	0.2
S5_R1_G12_FD	921,808	0.2
S5_R1_H12_FD	1,727,105	0.4
S5_R2_A01_FD	1,399,254	0.3
S5_R2_B01_FD	1,394,902	0.3
S5_R2_C01_FD	1,459,767	0.3
S5_R2_D01_FD	1,290,784	0.3
S5_R2_E01_FD	3,041,089	0.6
S5_R2_F01_FD	2,960,640	0.6
S5_R2_G01_FD	2,157,138	0.4
S5_R2_H01_FD	1,546,467	0.3
S5_R2_A02_FD	1,459,741	0.3
S5_R2_B02_FD	621,366	0.1
S5_R2_C02_FD	1,072,040	0.2
S5_R2_D02_FD	1,285,202	0.3
S5_R2_E02_FD	2,441,737	0.5
S5_R2_F02_FD	1,249,015	0.3
S5_R2_G02_FD	853,362	0.2
S5_R2_H02_FD	169,830	0.0
S5_R2_A03_FD	1,045,242	0.2
S5_R2_B03_FD	920,372	0.2
S5_R2_C03_FD	1,422,738	0.3
S5_R2_D03_FD	1,557,719	0.3
S5_R2_E03_FD	2,704,366	0.6
S5_R2_F03_FD	398,666	0.1
S5_R2_G03_FD	1,107,685	0.2
S5_R2_H03_FD	1,108,995	0.2
S5_R2_A04_FD	1,303,844	0.3
S5_R2_B04_FD	851,168	0.2
S5_R2_C04_FD	1,059,997	0.2
S5_R2_D04_FD	1,652,612	0.3
S5_R2_E04_FD	753,890	0.2
S5_R2_F04_FD	1,269,980	0.3
S5_R2_G04_FD	658,253	0.1
S5_R2_H04_FD	2,086,911	0.4
S5_R2_A05_FD	1,078,850	0.2
S5_R2_B05_FD	1,702,945	0.4
S5_R2_C05_FD	1,944,946	0.4
S5_R2_D05_FD	770,249	0.2
S5_R2_E05_FD	2,557,716	0.5
S5_R2_F05_FD	1,357,134	0.3
S5_R2_G05_FD	2,327,403	0.5
S5_R2_H05_FD	889,879	0.2
S5_R2_A06_FD	901,033	0.2
S5_R2_B06_FD	947,139	0.2
S5_R2_C06_FD	1,153,432	0.2
S5_R2_D06_FD	882,216	0.2
S5_R2_E06_FD	904,086	0.2
S5_R2_F06_FD	813,282	0.2
S5_R2_G06_FD	1,171,882	0.2
S5_R2_H06_FD	1,022,442	0.2
S5_R2_A07_FD	970,149	0.2
S5_R2_B07_FD	786,248	0.2
S5_R2_C07_FD	1,098,255	0.2
S5_R2_D07_FD	827,340	0.2
S5_R2_E07_FD	1,341,124	0.3
S5_R2_F07_FD	1,154,926	0.2
S5_R2_G07_FD	1,312,363	0.3
S5_R2_H07_FD	1,340,026	0.3
S5_R2_A08_FD	1,164,980	0.2
S5_R2_B08_FD	702,674	0.1
S5_R2_C08_FD	737,288	0.2
S5_R2_D08_FD	802,689	0.2
S5_R2_E08_FD	1,319,328	0.3
S5_R2_F08_FD	1,661,758	0.3
S5_R2_G08_FD	861,937	0.2
S5_R2_H08_FD	615,728	0.1
S5_R2_A09_FD	916,850	0.2
S5_R2_B09_FD	580,058	0.1
S5_R2_C09_FD	45,347	0.0
S5_R2_D09_FD	1,324,102	0.3
S5_R2_E09_FD	1,272,433	0.3
S5_R2_F09_FD	2,033,381	0.4
S5_R2_G09_FD	1,499,513	0.3
S5_R2_H09_FD	1,611,517	0.3
S5_R2_A10_FD	701,017	0.1
S5_R2_B10_FD	421,604	0.1
S5_R2_C10_FD	1,250,295	0.3
S5_R2_D10_FD	979,673	0.2
S5_R2_E10_FD	639,974	0.1
S5_R2_F10_FD	1,944,008	0.4
S5_R2_G10_FD	584,213	0.1
S5_R2_H10_FD	701,976	0.1
S5_R2_A11_FD	112,670	0.0
S5_R2_B11_FD	806,702	0.2
S5_R2_C11_FD	1,744,193	0.4
S5_R2_D11_FD	656,904	0.1
S5_R2_E11_FD	863,905	0.2
S5_R2_F11_FD	1,203,439	0.2
S5_R2_G11_FD	456,783	0.1
S5_R2_H11_FD	2,244,427	0.5
S5_R2_A12_FD	365,141	0.1
S5_R2_B12_FD	1,030,078	0.2
S5_R2_C12_FD	1,711,065	0.4
S5_R2_D12_FD	1,330,455	0.3
S5_R2_E12_FD	241,052	0.1
S5_R2_F12_FD	214,650	0.0
S5_R2_G12_FD	686,499	0.1
S5_R2_H12_FD	922,877	0.2
S6_R1_A01_FD	4,667,859	1.0
S6_R1_B01_FD	4,478,627	0.9
S6_R1_C01_FD	3,963,039	0.8
S6_R1_D01_FD	3,700,591	0.8
S6_R1_E01_FD	4,209,928	0.9
S6_R1_F01_FD	3,588,331	0.7
S6_R1_G01_FD	2,763,787	0.6
S6_R1_H01_FD	2,072,674	0.4
S6_R1_A02_FD	5,922,876	1.2
S6_R1_B02_FD	4,790,936	1.0
S6_R1_C02_FD	2,365,879	0.5
S6_R1_D02_FD	4,602,852	1.0
S6_R1_E02_FD	4,344,623	0.9
S6_R1_F02_FD	4,433,792	0.9
S6_R1_G02_FD	3,701,612	0.8
S6_R1_H02_FD	3,082,965	0.6
S6_R1_A03_FD	4,541,573	0.9
S6_R1_B03_FD	4,592,582	1.0
S6_R1_C03_FD	4,094,680	0.8
S6_R1_D03_FD	5,000,881	1.0
S6_R1_E03_FD	4,433,315	0.9
S6_R1_F03_FD	4,418,157	0.9
S6_R1_G03_FD	3,337,893	0.7
S6_R1_H03_FD	2,620,170	0.5
S6_R1_A04_FD	3,362,227	0.7
S6_R1_B04_FD	3,704,527	0.8
S6_R1_C04_FD	2,501,575	0.5
S6_R1_D04_FD	2,418,255	0.5
S6_R1_E04_FD	71.0	0.0
S6_R1_F04_FD	3,850,531	0.8
S6_R1_G04_FD	2,812,604	0.6
S6_R1_H04_FD	3,524,981	0.7
S6_R2_A01_FD	4,184,106	0.9
S6_R2_B01_FD	3,445,829	0.7
S6_R2_C01_FD	2,425,589	0.5
S6_R2_D01_FD	3,946,845	0.8
S6_R2_E01_FD	4,271,784	0.9
S6_R2_F01_FD	3,723,457	0.8
S6_R2_G01_FD	4,100,242	0.8
S6_R2_H01_FD	2,581,222	0.5
S6_R2_A02_FD	4,517,263	0.9
S6_R2_B02_FD	5,440,165	1.1
S6_R2_C02_FD	4,509,370	0.9
S6_R2_D02_FD	3,872,436	0.8
S6_R2_E02_FD	4,627,073	1.0
S6_R2_F02_FD	3,727,086	0.8
S6_R2_G02_FD	3,295,680	0.7
S6_R2_H02_FD	2,961,033	0.6
S6_R2_A03_FD	4,379,940	0.9
S6_R2_B03_FD	5,029,350	1.0
S6_R2_C03_FD	2,627,773	0.5
S6_R2_D03_FD	3,840,864	0.8
S6_R2_E03_FD	1,873,261	0.4
S6_R2_F03_FD	3,404,610	0.7
S6_R2_G03_FD	4,378,056	0.9
S6_R2_H03_FD	4,608,426	1.0
S6_R2_A04_FD	5,836,721	1.2
S6_R2_B04_FD	1,883,410	0.4
S6_R2_C04_FD	2,409,657	0.5
S6_R2_D04_FD	138,079	0.0
S6_R2_E04_FD	90,761	0.0
S6_R2_F04_FD	289,976	0.1
S6_R2_G04_FD	4,862,338	1.0
S6_R2_H04_FD	4,721,302	1.0

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|			Total Read Count	Total Read Count	`Total Read Count`	None
\|\|			Portion (%)	Portion (%)	`Portion (%)`	None

Barcodes of Undetermined Reads

Barcodes of Undetermined Reads
We have determined the barcodes of your undetermined reads (reads containing a barcode that you did not encode in your metadata). Here are the top 20 barcodes belonging to the undetermined reads. The full list is available here.

Showing ²⁰/₂₀ rows and ²/₂ columns.

Sample Name	Count	Frequency (%)
GGGGGGGGAGATCTCG	669320.0	4.1
GGGGGGGGCTAGTCGA	240481.0	1.5
GGGGGGGGAGCTAGAA	232771.0	1.4
GGGGGGGGGGGGGGGG	223574.0	1.4
GGGGGGGGATAGAGAG	220717.0	1.3
GGGGGGGGTACTCCTT	210904.0	1.3
GGGGGGGGATTAGACG	190379.0	1.2
GGGGGGGGACTCTAGG	184850.0	1.1
GGGGGGGGAGGCTTAG	183580.0	1.1
GGGGGGGGTCTTACGC	173207.0	1.1
GGGGGGGGTATGCAGT	167694.0	1.0
GGGGGGGGCGGAGAGA	165515.0	1.0
GGGGGGGGCTTAATAG	164304.0	1.0
GGGGGGGGTAAGGCTC	163864.0	1.0
GGGGGGGGATAGCCTT	159973.0	1.0
GGGGGGGGTCGCATAA	150117.0	0.9
GGGGGGGGAGAGGATA	148529.0	0.9
GGGGGGGGCTCCTTAC	144330.0	0.9
ACTCGCTAGGGGGGGG	105771.0	0.6
CGTACTAGGGGGGGGG	96777.0	0.6

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|			Count	Count	`Count`	None
\|\|			Frequency (%)	Frequency (%)	`Frequency (%)`	None

Run Statistics

Showing ¹/₁ rows and ⁴/₄ columns.

Sample Name	Total # of Single-End Reads	Total # PF Reads	% Undetermined	% PhiX Aligned
4.0	549,514,160	482,330,825	3.4	0.1

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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

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Per Base N Content

The percentage of base calls at each position for which an N was called. See the FastQC help.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Sequence Length Distribution

All samples have sequences of a single length (151bp).

Sequence Duplication Levels

The relative level of duplication found for every sequence. See the FastQC help.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Overrepresented sequences

The total amount of overrepresented sequences found in each library. See the FastQC help for further information.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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General Statistics

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Barcodes of Undetermined Reads

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Run Statistics

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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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