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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 1.6.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 2018-04-04, 08:52 based on data in: /mnt/owl/Athaliana/20180328_fastqc_trimmed_hiseq_geoduck

General Statistics

Showing ⁶⁴/₆₄ rows and ⁴/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
Geoduck-NMP-gDNA-1_S1_L001_R1_001_val_1	18.2%	34%	128 bp	17%	290.4
Geoduck-NMP-gDNA-1_S1_L001_R2_001_val_2	12.3%	35%	124 bp	25%	290.4
Geoduck-NMP-gDNA-2_S5_L002_R1_001_val_1	18.8%	34%	129 bp	8%	298.5
Geoduck-NMP-gDNA-2_S5_L002_R2_001_val_2	12.1%	35%	124 bp	17%	298.5
Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R1_001_val_1	0.1%	33%	137 bp	8%	0.0
Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R2_001_val_2	0.1%	34%	97 bp	25%	0.0
Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R1_001_val_1	0.1%	33%	137 bp	8%	0.0
Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R2_001_val_2	0.1%	34%	97 bp	25%	0.0
Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R1_001_val_1	12.7%	35%	129 bp	17%	284.3
Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R2_001_val_2	9.0%	36%	125 bp	25%	284.3
Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R1_001_val_1	12.6%	35%	129 bp	17%	288.0
Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R2_001_val_2	9.0%	36%	125 bp	17%	288.0
Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R1_001_val_1	0.2%	34%	131 bp	8%	0.2
Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R2_001_val_2	0.2%	35%	114 bp	8%	0.2
Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R1_001_val_1	0.5%	35%	130 bp	17%	0.2
Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R2_001_val_2	0.5%	35%	115 bp	8%	0.2
Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R1_001_val_1	7.5%	35%	126 bp	8%	0.4
Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R2_001_val_2	6.1%	36%	121 bp	8%	0.4
Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R1_001_val_1	6.3%	35%	126 bp	8%	0.4
Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R2_001_val_2	5.1%	36%	120 bp	17%	0.4
Geoduck-NMP-gDNA-3_S9_L003_R1_001_val_1	0.1%	34%	134 bp	8%	0.0
Geoduck-NMP-gDNA-3_S9_L003_R2_001_val_2	0.1%	32%	108 bp	17%	0.0
Geoduck-NMP-gDNA-4_S13_L004_R1_001_val_1	0.1%	34%	134 bp	8%	0.0
Geoduck-NMP-gDNA-4_S13_L004_R2_001_val_2	0.1%	32%	109 bp	8%	0.0
Geoduck-NMP-gDNA-5_S17_L005_R1_001_val_1	0.0%	35%	137 bp	8%	0.0
Geoduck-NMP-gDNA-5_S17_L005_R2_001_val_2	0.0%	37%	102 bp	17%	0.0
Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R1_001_val_1	0.1%	34%	135 bp	8%	0.0
Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R2_001_val_2	0.1%	34%	105 bp	17%	0.0
Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R1_001_val_1	0.1%	34%	135 bp	8%	0.1
Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R2_001_val_2	0.1%	33%	107 bp	17%	0.1
Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R1_001_val_1	0.6%	35%	136 bp	8%	0.8
Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R2_001_val_2	0.5%	36%	112 bp	17%	0.8
Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R1_001_val_1	0.5%	35%	135 bp	8%	0.7
Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R2_001_val_2	0.5%	36%	113 bp	8%	0.7
Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R1_001_val_1	11.8%	36%	121 bp	17%	235.8
Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R2_001_val_2	8.6%	36%	118 bp	25%	235.8
Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R1_001_val_1	11.8%	36%	121 bp	25%	237.9
Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R2_001_val_2	9.0%	36%	118 bp	17%	237.9
Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R1_001_val_1	0.4%	35%	133 bp	8%	0.2
Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R2_001_val_2	0.4%	35%	112 bp	8%	0.2
Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R1_001_val_1	0.4%	35%	133 bp	8%	0.3
Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R2_001_val_2	0.4%	35%	112 bp	8%	0.3
Geoduck-NMP-gDNA-6_S21_L006_R1_001_val_1	0.0%	35%	137 bp	17%	0.0
Geoduck-NMP-gDNA-6_S21_L006_R2_001_val_2	0.0%	37%	102 bp	17%	0.0
Geoduck-NMP-gDNA-7_S25_L007_R1_001_val_1	0.4%	36%	131 bp	17%	0.0
Geoduck-NMP-gDNA-7_S25_L007_R2_001_val_2	0.3%	37%	103 bp	17%	0.0
Geoduck-NMP-gDNA-8_S29_L008_R1_001_val_1	0.5%	36%	131 bp	17%	0.0
Geoduck-NMP-gDNA-8_S29_L008_R2_001_val_2	0.4%	37%	102 bp	17%	0.0
Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R1_001_val_1	0.4%	34%	137 bp	17%	0.0
Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R2_001_val_2	0.3%	36%	97 bp	17%	0.0
Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R1_001_val_1	0.4%	34%	136 bp	17%	0.0
Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R2_001_val_2	0.3%	35%	98 bp	17%	0.0
Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R1_001_val_1	3.2%	35%	130 bp	8%	0.2
Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R2_001_val_2	2.6%	35%	122 bp	17%	0.2
Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R1_001_val_1	3.1%	35%	130 bp	8%	0.2
Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R2_001_val_2	2.5%	35%	122 bp	8%	0.2
Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R1_001_val_1	0.1%	34%	134 bp	8%	0.1
Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R2_001_val_2	0.1%	35%	110 bp	8%	0.1
Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R1_001_val_1	0.0%	35%	134 bp	17%	0.1
Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R2_001_val_2	0.1%	35%	111 bp	8%	0.1
Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R1_001_val_1	15.8%	35%	125 bp	17%	281.5
Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R2_001_val_2	11.8%	36%	122 bp	17%	281.5
Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R1_001_val_1	15.7%	35%	126 bp	8%	286.0
Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R2_001_val_2	12.6%	36%	121 bp	25%	286.0

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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

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 sample 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

The distribution of fragment sizes (read lengths) found. See the FastQC help.

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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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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