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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

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 2017-10-28, 17:27 based on data in: /work/02189/rmharris/IntProWT/01_fastqc

General Statistics

Showing ¹⁰⁸/₁₀₈ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
142C_CA1_S_S19_L003_R1_001	87.9%	47%	151 bp	50%	12.0
142C_CA1_S_S19_L003_R2_001	78.6%	47%	151 bp	42%	12.0
142C_DG_S_S21_L003_R1_001	86.5%	48%	151 bp	50%	17.2
142C_DG_S_S21_L003_R2_001	77.6%	45%	151 bp	50%	17.2
143A_CA3_1_S35_L002_R1_001	80.5%	49%	151 bp	33%	5.8
143A_CA3_1_S35_L002_R2_001	71.0%	48%	151 bp	33%	5.8
143A_DG_1_S36_L002_R1_001	72.0%	50%	151 bp	42%	7.9
143A_DG_1_S36_L002_R2_001	63.1%	49%	151 bp	33%	7.9
143B_CA1_1_S37_L002_R1_001	71.3%	48%	151 bp	33%	2.9
143B_CA1_1_S37_L002_R2_001	62.4%	48%	151 bp	33%	2.9
143B_DG_1_S38_L002_R1_001	66.1%	49%	151 bp	42%	3.8
143B_DG_1_S38_L002_R2_001	58.0%	48%	151 bp	33%	3.8
143C_CA1_1_S39_L002_R1_001	64.2%	49%	151 bp	33%	3.5
143C_CA1_1_S39_L002_R2_001	55.9%	49%	151 bp	33%	3.5
143C_CA1_S_S20_L003_R1_001	66.5%	48%	151 bp	33%	10.8
143C_CA1_S_S20_L003_R2_001	60.0%	48%	151 bp	33%	10.8
143C_DG_S_S22_L003_R1_001	93.0%	48%	151 bp	58%	22.4
143C_DG_S_S22_L003_R2_001	85.5%	45%	151 bp	50%	22.4
143D_CA1_3_S40_L002_R1_001	84.7%	49%	151 bp	42%	3.2
143D_CA1_3_S40_L002_R2_001	75.0%	47%	151 bp	33%	3.2
143D_DG_3_S41_L002_R1_001	57.6%	48%	151 bp	33%	1.9
143D_DG_3_S41_L002_R2_001	49.3%	48%	151 bp	25%	1.9
144A_CA1_2_S42_L002_R1_001	62.2%	48%	151 bp	42%	4.9
144A_CA1_2_S42_L002_R2_001	56.0%	49%	151 bp	33%	4.9
144A_CA3_2_S43_L002_R1_001	63.2%	47%	151 bp	42%	1.8
144A_CA3_2_S43_L002_R2_001	55.9%	45%	151 bp	42%	1.8
144A_DG_2_S44_L002_R1_001	80.4%	49%	151 bp	42%	7.4
144A_DG_2_S44_L002_R2_001	70.4%	47%	151 bp	33%	7.4
144B_CA1_1_S45_L002_R1_001	79.9%	48%	151 bp	33%	4.3
144B_CA1_1_S45_L002_R2_001	70.4%	48%	151 bp	33%	4.3
144B_CA3_1_S46_L002_R1_001	96.3%	54%	151 bp	42%	24.9
144B_CA3_1_S46_L002_R2_001	88.2%	54%	151 bp	42%	24.9
144C_CA1_2_S47_L002_R1_001	69.5%	49%	151 bp	25%	5.3
144C_CA1_2_S47_L002_R2_001	62.0%	49%	151 bp	25%	5.3
144C_CA3_2_S48_L002_R1_001	85.7%	46%	151 bp	50%	4.4
144C_CA3_2_S48_L002_R2_001	78.4%	45%	151 bp	42%	4.4
144C_DG_2_S49_L002_R1_001	56.9%	48%	151 bp	42%	5.2
144C_DG_2_S49_L002_R2_001	50.5%	47%	151 bp	33%	5.2
144D_CA3_2_S50_L002_R1_001	74.6%	49%	151 bp	42%	4.7
144D_CA3_2_S50_L002_R2_001	66.1%	48%	151 bp	33%	4.7
144D_DG_2_S51_L002_R1_001	52.0%	49%	151 bp	33%	7.0
144D_DG_2_S51_L002_R2_001	46.7%	49%	151 bp	25%	7.0
145A_CA1_2_S52_L002_R1_001	79.3%	49%	151 bp	33%	7.2
145A_CA1_2_S52_L002_R2_001	70.2%	49%	151 bp	33%	7.2
145A_CA3_2_S53_L002_R1_001	91.4%	49%	151 bp	50%	3.1
145A_CA3_2_S53_L002_R2_001	85.0%	46%	151 bp	50%	3.1
145A_DG_2_S54_L002_R1_001	76.8%	49%	151 bp	42%	4.2
145A_DG_2_S54_L002_R2_001	69.7%	47%	151 bp	42%	4.2
145B_CA1_1_S55_L002_R1_001	82.6%	47%	151 bp	33%	4.1
145B_CA1_1_S55_L002_R2_001	72.7%	47%	151 bp	33%	4.1
145B_DG_1_S57_L002_R1_001	80.3%	48%	151 bp	42%	4.6
145B_DG_1_S57_L002_R2_001	70.4%	46%	151 bp	42%	4.6
146A_CA1_2_S58_L003_R1_001	65.0%	46%	151 bp	42%	3.6
146A_CA1_2_S58_L003_R2_001	54.3%	47%	151 bp	42%	3.6
146A_CA3_2_S59_L003_R1_001	85.4%	48%	151 bp	42%	5.9
146A_CA3_2_S59_L003_R2_001	74.6%	47%	151 bp	42%	5.9
146A_DG_2_S60_L003_R1_001	80.6%	48%	151 bp	50%	6.4
146A_DG_2_S60_L003_R2_001	67.7%	45%	151 bp	50%	6.4
146B_CA1_2_S61_L003_R1_001	93.8%	47%	151 bp	50%	13.5
146B_CA1_2_S61_L003_R2_001	84.0%	45%	151 bp	50%	13.5
146B_CA3_2_S62_L003_R1_001	74.2%	48%	151 bp	42%	3.9
146B_CA3_2_S62_L003_R2_001	63.6%	48%	151 bp	42%	3.9
146B_DG_2_S63_L003_R1_001	94.6%	47%	151 bp	50%	4.8
146B_DG_2_S63_L003_R2_001	86.1%	44%	151 bp	50%	4.8
146C_CA1_4_S64_L003_R1_001	71.6%	45%	151 bp	50%	9.4
146C_CA1_4_S64_L003_R2_001	63.7%	44%	151 bp	50%	9.4
146C_DG_4_S66_L003_R1_001	83.9%	47%	151 bp	50%	2.5
146C_DG_4_S66_L003_R2_001	74.5%	45%	151 bp	50%	2.5
146D_CA1_3_S67_L003_R1_001	94.0%	46%	151 bp	50%	5.7
146D_CA1_3_S67_L003_R2_001	86.2%	44%	151 bp	58%	5.7
146D_CA3_3_S68_L003_R1_001	86.1%	48%	151 bp	42%	6.7
146D_CA3_3_S68_L003_R2_001	72.0%	47%	151 bp	42%	6.7
146D_DG_3_S69_L003_R1_001	90.1%	46%	151 bp	50%	2.0
146D_DG_3_S69_L003_R2_001	81.3%	44%	151 bp	58%	2.0
147C_CA1_3_S70_L003_R1_001	71.7%	47%	151 bp	42%	7.5
147C_CA1_3_S70_L003_R2_001	61.8%	46%	151 bp	42%	7.5
147C_CA3_3_S71_L003_R1_001	86.2%	48%	151 bp	42%	8.7
147C_CA3_3_S71_L003_R2_001	73.6%	48%	151 bp	33%	8.7
147C_DG_3_S72_L003_R1_001	56.4%	49%	151 bp	33%	7.1
147C_DG_3_S72_L003_R2_001	48.2%	48%	151 bp	25%	7.1
147D_CA3_1_S74_L003_R1_001	85.1%	48%	151 bp	33%	8.4
147D_CA3_1_S74_L003_R2_001	74.1%	48%	151 bp	42%	8.4
147D_DG_1_S75_L003_R1_001	86.1%	49%	151 bp	42%	18.3
147D_DG_1_S75_L003_R2_001	74.5%	49%	151 bp	33%	18.3
147_CA1_4_S76_L003_R1_001	89.3%	46%	151 bp	42%	1.5
147_CA1_4_S76_L003_R2_001	78.2%	45%	151 bp	58%	1.5
147_CA3_4_S77_L003_R1_001	94.1%	48%	151 bp	50%	4.6
147_CA3_4_S77_L003_R2_001	85.3%	46%	151 bp	58%	4.6
147_DG_4_S78_L003_R1_001	94.2%	44%	151 bp	50%	4.0
147_DG_4_S78_L003_R2_001	82.9%	44%	151 bp	58%	4.0
148A_CA1_3_S79_L003_R1_001	68.9%	49%	151 bp	50%	8.1
148A_CA1_3_S79_L003_R2_001	61.8%	49%	151 bp	42%	8.1
148A_CA3_3_S80_L003_R1_001	81.4%	49%	151 bp	42%	5.7
148A_CA3_3_S80_L003_R2_001	70.2%	48%	151 bp	42%	5.7
148A_DG_3_S81_L003_R1_001	84.1%	49%	151 bp	42%	9.7
148A_DG_3_S81_L003_R2_001	72.5%	47%	151 bp	42%	9.7
148B_CA1_4_S82_L003_R1_001	90.3%	46%	151 bp	50%	2.6
148B_CA1_4_S82_L003_R2_001	81.1%	45%	151 bp	58%	2.6
148B_CA3_4_S83_L003_R1_001	93.9%	54%	151 bp	42%	37.9
148B_CA3_4_S83_L003_R2_001	85.7%	54%	151 bp	50%	37.9
148B_DG_4_S84_L003_R1_001	72.3%	49%	151 bp	33%	3.1
148B_DG_4_S84_L003_R2_001	63.8%	49%	151 bp	42%	3.1
148_CA1_2_S85_L003_R1_001	90.8%	47%	151 bp	42%	6.1
148_CA1_2_S85_L003_R2_001	79.1%	45%	151 bp	50%	6.1
148_CA3_2_S86_L003_R1_001	86.9%	47%	151 bp	42%	7.1
148_CA3_2_S86_L003_R2_001	75.4%	46%	151 bp	50%	7.1
148_DG_2_S87_L003_R1_001	88.1%	49%	151 bp	42%	5.1
148_DG_2_S87_L003_R2_001	76.4%	48%	151 bp	42%	5.1

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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.

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 sample row to see a line plot for that dataset.

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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.

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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.

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Overrepresented sequences

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

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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

General Statistics: Columns

FastQC

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Rollover for sample name

Per Sequence GC Content

Per Base N Content

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

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