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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 2017-10-31, 10:48 based on data in: /work/02189/rmharris/IntProWT/03_fastqc

General Statistics

Showing ¹⁰⁸/₁₀₈ rows and ⁴/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
142C_CA1_S_S19_L003_R1_001.filtrim	83.1%	48%	149 bp	25%	8.5
142C_CA1_S_S19_L003_R2_001.filtrim	75.0%	49%	150 bp	33%	8.5
142C_DG_S_S21_L003_R1_001.filtrim	68.9%	49%	146 bp	25%	7.5
142C_DG_S_S21_L003_R2_001.filtrim	58.6%	49%	149 bp	33%	7.5
143A_CA3_1_S35_L002_R1_001.filtrim	74.5%	50%	148 bp	17%	4.4
143A_CA3_1_S35_L002_R2_001.filtrim	63.9%	50%	150 bp	25%	4.4
143A_DG_1_S36_L002_R1_001.filtrim	66.7%	50%	148 bp	25%	6.7
143A_DG_1_S36_L002_R2_001.filtrim	57.3%	50%	150 bp	25%	6.7
143B_CA1_1_S37_L002_R1_001.filtrim	63.8%	49%	148 bp	17%	2.3
143B_CA1_1_S37_L002_R2_001.filtrim	54.1%	49%	150 bp	25%	2.3
143B_DG_1_S38_L002_R1_001.filtrim	59.0%	49%	148 bp	17%	3.1
143B_DG_1_S38_L002_R2_001.filtrim	50.2%	49%	150 bp	25%	3.1
143C_CA1_1_S39_L002_R1_001.filtrim	54.5%	50%	148 bp	17%	2.7
143C_CA1_1_S39_L002_R2_001.filtrim	45.4%	50%	150 bp	25%	2.7
143C_CA1_S_S20_L003_R1_001.filtrim	63.5%	49%	149 bp	25%	9.9
143C_CA1_S_S20_L003_R2_001.filtrim	57.1%	49%	150 bp	33%	9.9
143C_DG_S_S22_L003_R1_001.filtrim	77.6%	50%	144 bp	25%	7.0
143C_DG_S_S22_L003_R2_001.filtrim	65.0%	50%	148 bp	42%	7.0
143D_CA1_3_S40_L002_R1_001.filtrim	75.5%	49%	147 bp	25%	1.9
143D_CA1_3_S40_L002_R2_001.filtrim	62.9%	49%	150 bp	33%	1.9
143D_DG_3_S41_L002_R1_001.filtrim	49.9%	49%	148 bp	8%	1.6
143D_DG_3_S41_L002_R2_001.filtrim	41.8%	49%	150 bp	25%	1.6
144A_CA1_2_S42_L002_R1_001.filtrim	55.0%	49%	148 bp	25%	4.1
144A_CA1_2_S42_L002_R2_001.filtrim	49.2%	50%	150 bp	17%	4.1
144A_CA3_2_S43_L002_R1_001.filtrim	31.5%	46%	147 bp	8%	1.0
144A_CA3_2_S43_L002_R2_001.filtrim	25.3%	46%	150 bp	25%	1.0
144A_DG_2_S44_L002_R1_001.filtrim	68.5%	49%	147 bp	17%	4.5
144A_DG_2_S44_L002_R2_001.filtrim	58.2%	49%	150 bp	33%	4.5
144B_CA1_1_S45_L002_R1_001.filtrim	76.0%	49%	148 bp	25%	3.6
144B_CA1_1_S45_L002_R2_001.filtrim	66.1%	49%	150 bp	33%	3.6
144B_CA3_1_S46_L002_R1_001.filtrim	96.0%	55%	149 bp	42%	22.8
144B_CA3_1_S46_L002_R2_001.filtrim	88.6%	55%	150 bp	42%	22.8
144C_CA1_2_S47_L002_R1_001.filtrim	65.8%	50%	148 bp	17%	4.7
144C_CA1_2_S47_L002_R2_001.filtrim	57.9%	50%	150 bp	25%	4.7
144C_CA3_2_S48_L002_R1_001.filtrim	63.3%	49%	147 bp	17%	1.7
144C_CA3_2_S48_L002_R2_001.filtrim	53.1%	49%	150 bp	33%	1.7
144C_DG_2_S49_L002_R1_001.filtrim	34.2%	48%	146 bp	8%	3.5
144C_DG_2_S49_L002_R2_001.filtrim	29.1%	49%	150 bp	25%	3.5
144D_CA3_2_S50_L002_R1_001.filtrim	61.6%	50%	147 bp	17%	3.1
144D_CA3_2_S50_L002_R2_001.filtrim	52.2%	50%	150 bp	33%	3.1
144D_DG_2_S51_L002_R1_001.filtrim	44.5%	50%	148 bp	8%	6.1
144D_DG_2_S51_L002_R2_001.filtrim	39.2%	50%	150 bp	17%	6.1
145A_CA1_2_S52_L002_R1_001.filtrim	74.5%	50%	148 bp	17%	5.8
145A_CA1_2_S52_L002_R2_001.filtrim	64.9%	50%	150 bp	33%	5.8
145A_CA3_2_S53_L002_R1_001.filtrim	64.5%	46%	144 bp	33%	0.7
145A_CA3_2_S53_L002_R2_001.filtrim	51.3%	47%	148 bp	42%	0.7
145A_DG_2_S54_L002_R1_001.filtrim	51.9%	49%	148 bp	17%	2.0
145A_DG_2_S54_L002_R2_001.filtrim	42.5%	49%	150 bp	17%	2.0
145B_CA1_1_S55_L002_R1_001.filtrim	78.3%	48%	148 bp	25%	3.3
145B_CA1_1_S55_L002_R2_001.filtrim	67.6%	48%	150 bp	33%	3.3
145B_DG_1_S57_L002_R1_001.filtrim	62.5%	49%	148 bp	17%	2.4
145B_DG_1_S57_L002_R2_001.filtrim	51.6%	49%	150 bp	25%	2.4
146A_CA1_2_S58_L003_R1_001.filtrim	45.7%	49%	147 bp	8%	2.3
146A_CA1_2_S58_L003_R2_001.filtrim	39.0%	50%	150 bp	33%	2.3
146A_CA3_2_S59_L003_R1_001.filtrim	78.1%	48%	148 bp	25%	3.9
146A_CA3_2_S59_L003_R2_001.filtrim	66.0%	49%	150 bp	33%	3.9
146A_DG_2_S60_L003_R1_001.filtrim	30.3%	49%	144 bp	8%	1.8
146A_DG_2_S60_L003_R2_001.filtrim	20.7%	49%	149 bp	25%	1.8
146B_CA1_2_S61_L003_R1_001.filtrim	58.1%	49%	137 bp	33%	1.9
146B_CA1_2_S61_L003_R2_001.filtrim	42.4%	48%	146 bp	33%	1.9
146B_CA3_2_S62_L003_R1_001.filtrim	66.6%	49%	148 bp	17%	3.0
146B_CA3_2_S62_L003_R2_001.filtrim	55.6%	49%	150 bp	33%	3.0
146B_DG_2_S63_L003_R1_001.filtrim	62.9%	47%	139 bp	33%	0.6
146B_DG_2_S63_L003_R2_001.filtrim	50.2%	46%	146 bp	50%	0.6
146C_CA1_4_S64_L003_R1_001.filtrim	59.0%	44%	143 bp	25%	6.5
146C_CA1_4_S64_L003_R2_001.filtrim	51.0%	45%	150 bp	50%	6.5
146C_DG_4_S66_L003_R1_001.filtrim	54.5%	49%	145 bp	17%	0.9
146C_DG_4_S66_L003_R2_001.filtrim	43.6%	49%	149 bp	33%	0.9
146D_CA1_3_S67_L003_R1_001.filtrim	78.4%	48%	145 bp	25%	1.5
146D_CA1_3_S67_L003_R2_001.filtrim	65.5%	47%	149 bp	50%	1.5
146D_CA3_3_S68_L003_R1_001.filtrim	80.1%	48%	147 bp	33%	4.6
146D_CA3_3_S68_L003_R2_001.filtrim	65.8%	48%	150 bp	33%	4.6
146D_DG_3_S69_L003_R1_001.filtrim	64.8%	48%	146 bp	33%	0.5
146D_DG_3_S69_L003_R2_001.filtrim	53.7%	49%	149 bp	33%	0.5
147C_CA1_3_S70_L003_R1_001.filtrim	56.3%	48%	148 bp	25%	4.9
147C_CA1_3_S70_L003_R2_001.filtrim	46.5%	48%	150 bp	25%	4.9
147C_CA3_3_S71_L003_R1_001.filtrim	84.4%	48%	148 bp	25%	7.7
147C_CA3_3_S71_L003_R2_001.filtrim	71.2%	49%	150 bp	33%	7.7
147C_DG_3_S72_L003_R1_001.filtrim	49.8%	49%	148 bp	17%	6.2
147C_DG_3_S72_L003_R2_001.filtrim	41.2%	49%	150 bp	33%	6.2
147D_CA3_1_S74_L003_R1_001.filtrim	79.8%	49%	148 bp	17%	6.2
147D_CA3_1_S74_L003_R2_001.filtrim	67.3%	49%	150 bp	33%	6.2
147D_DG_1_S75_L003_R1_001.filtrim	84.2%	49%	149 bp	25%	16.1
147D_DG_1_S75_L003_R2_001.filtrim	71.4%	50%	150 bp	33%	16.1
147_CA1_4_S76_L003_R1_001.filtrim	78.3%	48%	147 bp	33%	0.7
147_CA1_4_S76_L003_R2_001.filtrim	65.5%	48%	150 bp	42%	0.7
147_CA3_4_S77_L003_R1_001.filtrim	85.2%	49%	146 bp	33%	1.7
147_CA3_4_S77_L003_R2_001.filtrim	70.2%	49%	149 bp	58%	1.7
147_DG_4_S78_L003_R1_001.filtrim	83.2%	50%	147 bp	33%	1.2
147_DG_4_S78_L003_R2_001.filtrim	69.0%	50%	149 bp	33%	1.2
148A_CA1_3_S79_L003_R1_001.filtrim	63.9%	50%	148 bp	33%	6.9
148A_CA1_3_S79_L003_R2_001.filtrim	57.0%	50%	150 bp	33%	6.9
148A_CA3_3_S80_L003_R1_001.filtrim	69.1%	50%	147 bp	17%	3.4
148A_CA3_3_S80_L003_R2_001.filtrim	56.7%	51%	150 bp	33%	3.4
148A_DG_3_S81_L003_R1_001.filtrim	74.5%	49%	148 bp	17%	6.0
148A_DG_3_S81_L003_R2_001.filtrim	62.0%	49%	150 bp	33%	6.0
148B_CA1_4_S82_L003_R1_001.filtrim	82.4%	47%	145 bp	33%	1.4
148B_CA1_4_S82_L003_R2_001.filtrim	73.4%	47%	150 bp	50%	1.4
148B_CA3_4_S83_L003_R1_001.filtrim	93.6%	54%	149 bp	42%	35.8
148B_CA3_4_S83_L003_R2_001.filtrim	85.7%	54%	150 bp	50%	35.8
148B_DG_4_S84_L003_R1_001.filtrim	66.8%	50%	149 bp	33%	2.6
148B_DG_4_S84_L003_R2_001.filtrim	57.9%	50%	150 bp	33%	2.6
148_CA1_2_S85_L003_R1_001.filtrim	82.3%	49%	148 bp	33%	3.1
148_CA1_2_S85_L003_R2_001.filtrim	68.2%	49%	150 bp	33%	3.1
148_CA3_2_S86_L003_R1_001.filtrim	71.4%	50%	147 bp	17%	3.2
148_CA3_2_S86_L003_R2_001.filtrim	58.3%	50%	150 bp	33%	3.2
148_DG_2_S87_L003_R1_001.filtrim	83.2%	49%	148 bp	33%	3.5
148_DG_2_S87_L003_R2_001.filtrim	69.5%	49%	150 bp	33%	3.5

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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.

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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.

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%T: -

%C: -

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%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.

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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

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

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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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