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 2022-10-13, 09:10 based on data in: /mainfs/scratch/cmp1g20/Neuroblastoma_RNAseq/FASTQC

General Statistics

Showing ¹⁰⁸/₁₀₈ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
COMB1_PT10_1_1	67.4%	50%	150	18%	43.0
COMB1_PT10_1_2	65.4%	50%	150	18%	43.0
COMB1_PT10_2_1	71.7%	51%	150	18%	43.3
COMB1_PT10_2_2	68.7%	51%	150	18%	43.3
COMB1_PT10_3_1	58.6%	50%	150	18%	45.1
COMB1_PT10_3_2	55.9%	50%	150	18%	45.1
COMB1_PT3_1_1	67.0%	50%	150	18%	43.7
COMB1_PT3_1_2	64.4%	50%	150	18%	43.7
COMB1_PT3_2_1	67.2%	50%	150	18%	42.9
COMB1_PT3_2_2	64.9%	50%	150	18%	42.9
COMB1_PT3_3_1	60.1%	51%	150	18%	55.8
COMB1_PT3_3_2	57.8%	51%	150	18%	55.8
COMB1_PT7_1_1	65.5%	51%	150	18%	45.9
COMB1_PT7_1_2	64.4%	51%	150	18%	45.9
COMB1_PT7_2_1	68.2%	52%	150	18%	41.2
COMB1_PT7_2_2	64.3%	52%	150	18%	41.2
COMB1_PT7_3_1	55.7%	51%	150	18%	42.9
COMB1_PT7_3_2	53.6%	51%	150	18%	42.9
COMB2_PT10_1_1	75.0%	49%	150	18%	44.2
COMB2_PT10_1_2	72.7%	49%	150	18%	44.2
COMB2_PT10_2_1	67.5%	52%	150	18%	44.1
COMB2_PT10_2_2	65.7%	52%	150	18%	44.1
COMB2_PT10_3_1	63.0%	48%	150	18%	43.5
COMB2_PT10_3_2	61.4%	48%	150	18%	43.5
COMB2_PT3_1_1	67.7%	50%	150	18%	53.1
COMB2_PT3_1_2	66.4%	50%	150	18%	53.1
COMB2_PT3_2_1	67.8%	51%	150	18%	46.2
COMB2_PT3_2_2	64.3%	51%	150	18%	46.2
COMB2_PT3_3_1	58.4%	51%	150	18%	41.6
COMB2_PT3_3_2	56.5%	51%	150	18%	41.6
COMB2_PT7_1_1	65.8%	51%	150	18%	41.5
COMB2_PT7_1_2	64.8%	51%	150	18%	41.5
COMB2_PT7_2_1	71.6%	46%	150	18%	42.2
COMB2_PT7_2_2	71.0%	46%	150	18%	42.2
COMB2_PT7_3_1	58.8%	52%	150	18%	43.0
COMB2_PT7_3_2	57.1%	52%	150	18%	43.0
DMSO_PT10_1_1	70.8%	52%	150	18%	40.6
DMSO_PT10_1_2	69.0%	52%	150	18%	40.6
DMSO_PT10_2_1	76.5%	48%	150	18%	42.7
DMSO_PT10_2_2	75.1%	48%	150	18%	42.7
DMSO_PT10_3_1	58.7%	52%	150	18%	42.8
DMSO_PT10_3_2	56.5%	52%	150	18%	42.8
DMSO_PT3_1_1	67.8%	49%	150	18%	48.0
DMSO_PT3_1_2	66.8%	50%	150	18%	48.0
DMSO_PT3_2_1	71.2%	51%	150	18%	55.2
DMSO_PT3_2_2	68.8%	51%	150	18%	55.2
DMSO_PT3_3_1	59.9%	51%	150	18%	47.1
DMSO_PT3_3_2	56.5%	51%	150	18%	47.1
DMSO_PT7_1_1	68.7%	51%	150	18%	48.0
DMSO_PT7_1_2	67.5%	51%	150	18%	48.0
DMSO_PT7_2_1	70.2%	52%	150	18%	56.1
DMSO_PT7_2_2	68.5%	52%	150	18%	56.1
DMSO_PT7_3_1	58.6%	51%	150	18%	41.9
DMSO_PT7_3_2	56.1%	51%	150	18%	41.9
GSK_PT10_1_1	74.0%	49%	150	18%	42.1
GSK_PT10_1_2	72.5%	49%	150	18%	42.1
GSK_PT10_2_1	72.7%	50%	150	18%	41.0
GSK_PT10_2_2	71.6%	50%	150	18%	41.0
GSK_PT10_3_1	61.4%	48%	150	18%	43.0
GSK_PT10_3_2	60.3%	48%	150	18%	43.0
GSK_PT3_1_1	74.5%	51%	150	18%	42.0
GSK_PT3_1_2	74.6%	51%	150	18%	42.0
GSK_PT3_2_1	69.7%	51%	150	18%	48.1
GSK_PT3_2_2	68.5%	51%	150	18%	48.1
GSK_PT3_3_1	61.1%	51%	150	18%	55.2
GSK_PT3_3_2	58.3%	51%	150	18%	55.2
GSK_PT7_1_1	63.1%	51%	150	18%	40.5
GSK_PT7_1_2	62.4%	51%	150	18%	40.5
GSK_PT7_2_1	66.5%	52%	150	18%	41.8
GSK_PT7_2_2	63.7%	52%	150	18%	41.8
GSK_PT7_3_1	57.6%	50%	150	18%	41.1
GSK_PT7_3_2	55.9%	50%	150	18%	41.1
RA_PT10_1_1	71.2%	51%	150	18%	42.0
RA_PT10_1_2	69.5%	51%	150	18%	42.0
RA_PT10_2_1	69.0%	50%	150	18%	41.1
RA_PT10_2_2	66.7%	50%	150	18%	41.1
RA_PT10_3_1	60.4%	51%	150	18%	42.2
RA_PT10_3_2	56.9%	51%	150	18%	42.2
RA_PT3_1_1	68.2%	49%	150	18%	48.2
RA_PT3_1_2	66.1%	49%	150	18%	48.2
RA_PT3_2_1	68.5%	51%	150	18%	41.9
RA_PT3_2_2	66.6%	51%	150	18%	41.9
RA_PT3_3_1	59.0%	51%	150	18%	46.7
RA_PT3_3_2	57.3%	51%	150	18%	46.7
RA_PT7_1_1	66.4%	51%	150	18%	46.8
RA_PT7_1_2	65.0%	51%	150	18%	46.8
RA_PT7_2_1	67.3%	52%	150	18%	41.9
RA_PT7_2_2	65.4%	52%	150	18%	41.9
RA_PT7_3_1	64.9%	50%	150	18%	43.4
RA_PT7_3_2	64.2%	50%	150	18%	43.4
TAZ_PT10_1_1	68.8%	51%	150	18%	40.8
TAZ_PT10_1_2	67.4%	51%	150	18%	40.8
TAZ_PT10_2_1	74.1%	49%	150	18%	42.0
TAZ_PT10_2_2	71.6%	49%	150	18%	42.0
TAZ_PT10_3_1	60.2%	50%	150	18%	41.5
TAZ_PT10_3_2	58.4%	50%	150	18%	41.5
TAZ_PT3_1_1	67.9%	51%	150	18%	41.7
TAZ_PT3_1_2	65.3%	51%	150	18%	41.7
TAZ_PT3_2_1	69.9%	50%	150	18%	48.2
TAZ_PT3_2_2	68.2%	50%	150	18%	48.2
TAZ_PT3_3_1	58.9%	51%	150	18%	48.0
TAZ_PT3_3_2	56.5%	51%	150	18%	48.0
TAZ_PT7_1_1	64.8%	51%	150	18%	43.0
TAZ_PT7_1_2	63.9%	51%	150	18%	43.0
TAZ_PT7_2_1	67.9%	52%	150	18%	40.6
TAZ_PT7_2_2	64.1%	52%	150	18%	40.6
TAZ_PT7_3_1	57.4%	51%	150	18%	43.5
TAZ_PT7_3_2	55.5%	51%	150	18%	43.5

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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: -

%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.

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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

All samples have sequences of a single length (150bp).

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.

108 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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