MultiQC Report

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

Report generated on 2020-09-22, 16:09 based on data in: /beegfs/mk5636/logs/html/HNG7HBGXG/merged

General Statistics

Showing 572 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 ²⁸⁶/₂₈₆ rows and ²/₂ columns.

Sample Name	Total Read Count	Portion (%)
undetermined_library	34,315,222	6.8
2233_d02_replicate1	1,605,394	0.3
2230_d02_replicate1	1,550,126	0.3
2232_d04_replicate1	1,536,969	0.3
2241_d06_replicate1	1,468,742	0.3
2254_d08_replicate1	1,356,960	0.3
2241_d10_replicate1	1,373,646	0.3
2231_d10_replicate1	1,383,419	0.3
2238_d12_replicate1	1,424,098	0.3
2234_d02_replicate1	1,523,031	0.3
2235_d02_replicate1	1,582,445	0.3
2235_d04_replicate1	1,514,417	0.3
2253_d06_replicate1	1,592,966	0.3
2251_d08_replicate1	1,334,525	0.3
2238_d10_replicate1	1,593,111	0.3
2254_d10_replicate1	1,599,106	0.3
2254_d12_replicate1	1,433,141	0.3
2232_d02_replicate1	1,276,080	0.3
2237_d02_replicate1	1,479,441	0.3
2230_d04_replicate1	1,544,223	0.3
2239_d06_replicate1	1,544,715	0.3
2230_d08_replicate1	1,703,483	0.3
2232_d10_replicate1	1,641,252	0.3
2230_d12_replicate1	1,564,021	0.3
2243_d12_replicate1	1,715,853	0.3
2251_d02_replicate1	1,427,423	0.3
2240_d04_replicate1	1,809,523	0.4
2238_d04_replicate1	861,207	0.2
2240_d06_replicate1	1,423,257	0.3
2253_d08_replicate1	389,510	0.1
2243_d10_replicate1	1,716,721	0.3
2237_d12_replicate1	1,561,389	0.3
2244_d12_replicate1	1,231,334	0.2
2254_d02_replicate1	1,656,640	0.3
2253_d04_replicate1	1,547,916	0.3
2254_d04_replicate1	1,402,576	0.3
2238_d06_replicate1	1,634,426	0.3
2237_d08_replicate1	1,613,049	0.3
2237_d10_replicate1	1,878,156	0.4
2232_d12_replicate1	1,384,230	0.3
2246_d12_replicate1	1,419,591	0.3
2238_d02_replicate1	1,567,259	0.3
2241_d04_replicate1	1,566,890	0.3
2251_d04_replicate1	1,458,786	0.3
2254_d06_replicate1	1,331,264	0.3
2241_d08_replicate1	1,655,100	0.3
2230_d10_replicate1	1,318,428	0.3
2235_d12_replicate1	1,586,011	0.3
2246_d08.2_replicate1	1,489,484	0.3
2253_d02_replicate1	1,611,116	0.3
2234_d04_replicate1	1,474,789	0.3
2232_d06_replicate1	1,284,170	0.3
2231_d06_replicate1	1,475,965	0.3
2242_d08_replicate1	1,520,573	0.3
2235_d10_replicate1	1,718,325	0.3
2242_d12_replicate1	1,533,840	0.3
2244_d08.2_replicate1	1,823,071	0.4
2241_d02_replicate1	1,563,485	0.3
2242_d04_replicate1	1,760,647	0.4
2235_d06_replicate1	1,451,507	0.3
2234_d06_replicate1	1,319,012	0.3
2243_d08_replicate1	1,600,524	0.3
2244_d10_replicate1	1,658,737	0.3
2239_d12_replicate1	1,051,967	0.2
2248_d08.2_replicate1	1,704,077	0.3
2240_d02_replicate1	1,608,011	0.3
2239_d04_replicate1	1,716,610	0.3
2237_d06_replicate1	1,696,922	0.3
2233_d06_replicate1	34.0	0.0
2232_d08_replicate1	1,756,428	0.3
2242_d10_replicate1	1,560,645	0.3
2241_d12_replicate1	1,587,062	0.3
Blank_Control_replicate1	50.0	0.0
2231_d02_replicate1	1,595,182	0.3
2231_d04_replicate1	1,642,887	0.3
2230_d06_replicate1	1,535,721	0.3
2231_d08_replicate1	1,579,104	0.3
2238_d08_replicate1	1,774,266	0.4
2246_d10_replicate1	1,777,390	0.4
2253_d12_replicate1	1,685,157	0.3
HK1073_99_replicate1	1,520,823	0.3
2242_d02_replicate1	1,632,215	0.3
2237_d04_replicate1	1,750,382	0.3
2251_d06_replicate1	852,860	0.2
2044_d08_replicate1	1,685,406	0.3
2239_d08_replicate1	1,841,428	0.4
2239_d10_replicate1	1,814,822	0.4
2251_d12_replicate1	1,849,356	0.4
Blank_Space_replicate1	1,733,840	0.3
2339_d02_replicate1	2,502,937	0.5
2233_d04_replicate1	1,799,974	0.4
2242_d06_replicate1	1,493,971	0.3
2246_d08_replicate1	1,748,293	0.3
2251_d10_replicate1	1,549,294	0.3
2253_d10_replicate1	1,908,897	0.4
2231_d12_replicate1	1,775,597	0.4
pDZ_PB2_replicate1	1,882,966	0.4
2233_d02_replicate2	2,044,571	0.4
2230_d02_replicate2	1,889,911	0.4
2232_d04_replicate2	704,636	0.1
2241_d06_replicate2	1,997,385	0.4
2254_d08_replicate2	1,675,204	0.3
2241_d10_replicate2	1,951,320	0.4
2231_d10_replicate2	1,309,103	0.3
2238_d12_replicate2	1,278,205	0.3
2234_d02_replicate2	2,118,153	0.4
2235_d02_replicate2	1,812,093	0.4
2235_d04_replicate2	1,561,233	0.3
2253_d06_replicate2	1,887,660	0.4
2251_d08_replicate2	1,491,640	0.3
2238_d10_replicate2	2,013,845	0.4
2254_d10_replicate2	1,746,468	0.3
2254_d12_replicate2	104.0	0.0
2232_d02_replicate2	2,317,517	0.5
2237_d02_replicate2	2,031,457	0.4
2230_d04_replicate2	1,888,383	0.4
2239_d06_replicate2	1,865,219	0.4
2230_d08_replicate2	1,874,269	0.4
2232_d10_replicate2	1,410,196	0.3
2230_d12_replicate2	1,686,794	0.3
2243_d12_replicate2	1,473,173	0.3
2251_d02_replicate2	1,988,040	0.4
2240_d04_replicate2	1,782,844	0.4
2238_d04_replicate2	1,307,487	0.3
2240_d06_replicate2	1,480,168	0.3
2253_d08_replicate2	1,429,619	0.3
2243_d10_replicate2	1,516,959	0.3
2237_d12_replicate2	2,112,849	0.4
2244_d12_replicate2	1,801,125	0.4
2254_d02_replicate2	2,122,319	0.4
2253_d04_replicate2	1,819,100	0.4
2254_d04_replicate2	603,266	0.1
2238_d06_replicate2	1,227,451	0.2
2237_d08_replicate2	1,869,717	0.4
2237_d10_replicate2	1,822,332	0.4
2232_d12_replicate2	1,372,124	0.3
2246_d12_replicate2	1,871,826	0.4
2238_d02_replicate2	2,121,606	0.4
2241_d04_replicate2	2,182,676	0.4
2251_d04_replicate2	882,299	0.2
2254_d06_replicate2	1,400,656	0.3
2241_d08_replicate2	1,019,097	0.2
2230_d10_replicate2	1,793,854	0.4
2235_d12_replicate2	869,006	0.2
2246_d08.2_replicate2	1,361,875	0.3
2253_d02_replicate2	2,144,437	0.4
2234_d04_replicate2	1,914,651	0.4
2232_d06_replicate2	1,816,124	0.4
2231_d06_replicate2	1,761,173	0.4
2242_d08_replicate2	2,197,542	0.4
2235_d10_replicate2	1,370,147	0.3
2242_d12_replicate2	2,083,633	0.4
2244_d08.2_replicate2	659,227	0.1
2241_d02_replicate2	2,078,769	0.4
2242_d04_replicate2	1,905,536	0.4
2235_d06_replicate2	1,424,653	0.3
2234_d06_replicate2	1,906,344	0.4
2243_d08_replicate2	2,024,366	0.4
2244_d10_replicate2	1,908,074	0.4
2239_d12_replicate2	1,683,660	0.3
2248_d08.2_replicate2	2,360,107	0.5
2240_d02_replicate2	2,756,425	0.6
2239_d04_replicate2	1,959,426	0.4
2237_d06_replicate2	1,027,534	0.2
2233_d06_replicate2	1,318,331	0.3
2232_d08_replicate2	1,233,794	0.2
2242_d10_replicate2	2,153,984	0.4
2241_d12_replicate2	1,965,598	0.4
Blank_Control_replicate2	280,562	0.1
2231_d02_replicate2	2,481,649	0.5
2231_d04_replicate2	1,864,495	0.4
2230_d06_replicate2	2,132,673	0.4
2231_d08_replicate2	1,676,474	0.3
2238_d08_replicate2	1,893,274	0.4
2246_d10_replicate2	2,064,035	0.4
2253_d12_replicate2	2,029,873	0.4
HK1073_99_replicate2	2,153,982	0.4
2242_d02_replicate2	2,480,642	0.5
2237_d04_replicate2	2,323,682	0.5
2251_d06_replicate2	1,943,286	0.4
2044_d08_replicate2	1,662,694	0.3
2239_d08_replicate2	2,016,821	0.4
2239_d10_replicate2	2,263,524	0.5
2251_d12_replicate2	2,006,561	0.4
Blank_Space_replicate2	183.0	0.0
2339_d02_replicate2	2,313,690	0.5
2233_d04_replicate2	2,326,314	0.5
2242_d06_replicate2	1,525,633	0.3
2246_d08_replicate2	2,307,136	0.5
2251_d10_replicate2	2,370,621	0.5
2253_d10_replicate2	2,436,404	0.5
2231_d12_replicate2	2,642,302	0.5
pDZ_PB2_replicate2	1,530,420	0.3
1787_d02_replicate2	1,618,102	0.3
1788_d02_replicate2	1,475,383	0.3
1789_d02_replicate2	913,292	0.2
1790_d02_replicate2	911,599	0.2
1793_d02_replicate2	1,233,669	0.2
1794_d02_replicate2	1,592,421	0.3
1795_d02_replicate2	1,531,585	0.3
1796_d02_replicate2	2,203,230	0.4
1797_d02_replicate2	2,084,721	0.4
1800_d02_replicate2	953,547	0.2
1801_d02_replicate2	3,087,906	0.6
1802_d02_replicate2	3,354,101	0.7
1803_d02_replicate2	1,726,538	0.3
1805_d02_replicate2	1,380,123	0.3
1787_d04_replicate2	1,249,892	0.2
1788_d04_replicate2	1,228,071	0.2
1789_d04_replicate2	1,474,878	0.3
1790_d04_replicate2	1,826,357	0.4
1793_d04_replicate2	1,845,756	0.4
1794_d04_replicate2	2,102,489	0.4
1795_d04_replicate2	2,244,018	0.4
1796_d04_replicate2	11,399,471	2.3
1797_d04_replicate2	2,465,459	0.5
1800_d04_replicate2	2,964,291	0.6
1801_d04_replicate2	1,448,439	0.3
1802_d04_replicate2	58,412	0.0
1803_d04_replicate2	1,242,019	0.2
1805_d04_replicate2	1,085,802	0.2
1787_d06_replicate2	1,438,254	0.3
1788_d06_replicate2	1,324,461	0.3
1789_d06_replicate2	2,142,410	0.4
1790_d06_replicate2	381,123	0.1
1793_d06_replicate2	1,920,671	0.4
1794_d06_replicate2	2,292,540	0.5
1795_d06_replicate2	1,932,667	0.4
1796_d06_replicate2	1,682,579	0.3
1794_d08_replicate2	1,315,638	0.3
1793_d08_replicate2	467,062	0.1
1790_d08_replicate2	866,342	0.2
1789_d08_replicate2	1,339,660	0.3
1788_d08_replicate2	1,559,903	0.3
1787_d08_replicate2	1,176,232	0.2
1805_d06_replicate2	1,817,227	0.4
1803_d06_replicate2	1,469,131	0.3
1802_d06_replicate2	2,311,821	0.5
1801_d06_replicate2	1,953,840	0.4
1800_d06_replicate2	2,466,007	0.5
1797_d06_replicate2	2,332,468	0.5
1795_d08_replicate2	1,495,074	0.3
1796_d08_replicate2	1,127,400	0.2
1797_d08_replicate2	961,356	0.2
1800_d08_replicate2	1,187,882	0.2
1801_d08_replicate2	1,927,375	0.4
1802_d08_replicate2	1,818,900	0.4
1803_d08_replicate2	2,240,103	0.4
1805_d08_replicate2	1,790,336	0.4
1787_d10_replicate2	2,108,537	0.4
1788_d10_replicate2	1,757,628	0.3
1789_d10_replicate2	2,643,749	0.5
1790_d10_replicate2	1,372,779	0.3
1793_d10_replicate2	1,985,839	0.4
1794_d10_replicate2	1,164,955	0.2
1795_d10_replicate2	545,083	0.1
1796_d10_replicate2	1,298,516	0.3
1797_d10_replicate2	1,639,453	0.3
1800_d10_replicate2	1,476,110	0.3
1801_d10_replicate2	2,433,537	0.5
1802_d10_replicate2	1,993,914	0.4
1803_d10_replicate2	2,051,415	0.4
1805_d10_replicate2	2,791,470	0.6
1787_d12_replicate2	3,139,181	0.6
1788_d12_replicate2	2,926,564	0.6
1789_d12_replicate2	1,233,811	0.2
1790_d12_replicate2	1,321,709	0.3
1793_d12_replicate2	1,349,519	0.3
1794_d12_replicate2	1,053,027	0.2
1795_d12_replicate2	1,822,411	0.4
1796_d12_replicate2	1,563,697	0.3
1797_d12_replicate2	1,520,734	0.3
1800_d12_replicate2	1,422,485	0.3
1801_d12_replicate2	1,600,793	0.3
1802_d12_replicate2	1,394,206	0.3
1803_d12_replicate2	672,496	0.1
1805_d12_replicate2	2,803,606	0.6
1787_d8eye_replicate2	4,736	0.0
1794_d10eye_replicate2	4,563	0.0
Negative_Control_replicate2	19.0	0.0
AHK1073_99_replicate2	100,794	0.0
Chang_06_replicate2	36,408	0.0
Chang_07_replicate2	6,124	0.0
Chang_08_replicate2	651,323	0.1
pDZPB2_nonamp_replicate2	49,816	0.0
pDZPB2_amp_replicate2	1,132,187	0.2

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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	14407256.0	42.0
NNNNNNNNNNNNNNNN	1320206.0	3.9
GGGGGGGGTACTCCTT	394641.0	1.1
GGGGGGGGAGGCTTAG	350303.0	1.0
GGGGGGGGTATGCAGT	349021.0	1.0
GGGGGGGGAGCTAGAA	340554.0	1.0
GGGGGGGGATAGAGAG	330259.0	1.0
GGGGGGGGATTAGACG	326049.0	0.9
GGGGGGGGAGAGGATA	317751.0	0.9
GGGGGGGGCTCCTTAC	277606.0	0.8
GGGGGGGGCTAGTCGA	257711.0	0.8
GGGGGGGGATAGCCTT	228670.0	0.7
GGGGGGGGTCTTACGC	227914.0	0.7
GGGGGGGGCGGAGAGA	227448.0	0.7
GGGGGGGGCTTAATAG	222579.0	0.7
GGGGGGGGAGCTCTCG	194876.0	0.6
GGGGGGGGACTCTAGG	165681.0	0.5
GGGGGGGGTAAGGCTC	160422.0	0.5
GGGGGGGGGGGGGGGG	103338.0	0.3
ACTCGCTAGGGGGGGG	80207.0	0.2

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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	559,199,952	501,677,417	6.8	2.9

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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

Run Statistics

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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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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