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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 1.5.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 2018-05-16, 14:51 based on data in: /home/sam/analyses/20180516_geoduck_EPI_fastqc

General Statistics

Showing ¹⁰⁶/₁₀₆ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
EPI-103_S27_L005_R1_001	17.3%	25%	101 bp	18%	20.4
EPI-103_S27_L005_R2_001	18.7%	26%	101 bp	27%	20.4
EPI-104_S28_L005_R1_001	17.9%	26%	101 bp	18%	30.2
EPI-104_S28_L005_R2_001	20.5%	26%	101 bp	27%	30.2
EPI-111_S29_L005_R1_001	17.7%	26%	101 bp	18%	27.1
EPI-111_S29_L005_R2_001	19.8%	26%	101 bp	27%	27.1
EPI-113_S30_L005_R1_001	19.9%	26%	101 bp	18%	26.4
EPI-113_S30_L005_R2_001	21.9%	26%	101 bp	27%	26.4
EPI-119_S31_L005_R1_001	20.8%	26%	101 bp	18%	29.0
EPI-119_S31_L005_R2_001	23.8%	26%	101 bp	27%	29.0
EPI-120_S32_L005_R1_001	17.5%	25%	101 bp	18%	24.2
EPI-120_S32_L005_R2_001	19.9%	26%	101 bp	27%	24.2
EPI-127_S33_L005_R1_001	19.2%	25%	101 bp	18%	22.4
EPI-127_S33_L005_R2_001	21.2%	26%	101 bp	27%	22.4
EPI-128_S34_L005_R1_001	19.9%	26%	101 bp	18%	24.7
EPI-128_S34_L005_R2_001	22.2%	26%	101 bp	27%	24.7
EPI-135WG_S42_L005_R1_001	54.3%	27%	101 bp	27%	176.8
EPI-135WG_S42_L005_R2_001	57.9%	27%	101 bp	27%	176.8
EPI-135_S35_L005_R1_001	20.8%	27%	101 bp	18%	29.0
EPI-135_S35_L005_R2_001	23.9%	27%	101 bp	27%	29.0
EPI-136_S36_L005_R1_001	19.0%	27%	101 bp	18%	27.9
EPI-136_S36_L005_R2_001	21.8%	27%	101 bp	27%	27.9
EPI-143_S37_L005_R1_001	17.6%	26%	101 bp	18%	21.3
EPI-143_S37_L005_R2_001	19.2%	26%	101 bp	27%	21.3
EPI-145_S38_L005_R1_001	20.4%	26%	101 bp	18%	25.5
EPI-145_S38_L005_R2_001	23.1%	26%	101 bp	27%	25.5
EPI-151_S2_L002_R1_001	39.6%	30%	101 bp	18%	29.6
EPI-151_S2_L002_R2_001	41.8%	31%	101 bp	27%	29.6
EPI-152_S3_L002_R1_001	29.8%	27%	101 bp	18%	30.3
EPI-152_S3_L002_R2_001	33.8%	28%	101 bp	18%	30.3
EPI-153_S4_L002_R1_001	46.7%	31%	101 bp	27%	31.8
EPI-153_S4_L002_R2_001	48.3%	32%	101 bp	27%	31.8
EPI-154_S5_L002_R1_001	28.3%	27%	101 bp	18%	25.4
EPI-154_S5_L002_R2_001	31.7%	28%	101 bp	18%	25.4
EPI-159_S6_L002_R1_001	30.2%	28%	101 bp	18%	16.0
EPI-159_S6_L002_R2_001	31.6%	28%	101 bp	18%	16.0
EPI-160_S7_L002_R1_001	32.0%	30%	101 bp	18%	34.2
EPI-160_S7_L002_R2_001	35.4%	30%	101 bp	18%	34.2
EPI-161_S8_L002_R1_001	26.9%	29%	101 bp	18%	24.9
EPI-161_S8_L002_R2_001	28.7%	29%	101 bp	18%	24.9
EPI-162_S9_L002_R1_001	23.9%	29%	101 bp	18%	23.4
EPI-162_S9_L002_R2_001	26.2%	30%	101 bp	18%	23.4
EPI-167_S10_L002_R1_001	28.1%	26%	101 bp	18%	24.9
EPI-167_S10_L002_R2_001	30.6%	27%	101 bp	18%	24.9
EPI-168_S11_L002_R1_001	30.0%	27%	101 bp	18%	23.3
EPI-168_S11_L002_R2_001	34.2%	28%	101 bp	18%	23.3
EPI-169_S12_L002_R1_001	25.5%	30%	101 bp	18%	21.8
EPI-169_S12_L002_R2_001	28.8%	30%	101 bp	18%	21.8
EPI-170_S13_L002_R1_001	25.1%	29%	101 bp	18%	28.3
EPI-170_S13_L002_R2_001	27.8%	30%	101 bp	18%	28.3
EPI-175_S14_L003_R1_001	25.0%	27%	101 bp	27%	25.2
EPI-175_S14_L003_R2_001	28.0%	28%	101 bp	18%	25.2
EPI-176_S15_L003_R1_001	28.4%	27%	101 bp	27%	36.6
EPI-176_S15_L003_R2_001	31.5%	27%	101 bp	18%	36.6
EPI-181_S16_L003_R1_001	26.9%	27%	101 bp	27%	27.6
EPI-181_S16_L003_R2_001	30.8%	28%	101 bp	18%	27.6
EPI-182_S17_L003_R1_001	25.0%	27%	101 bp	27%	32.1
EPI-182_S17_L003_R2_001	27.6%	27%	101 bp	18%	32.1
EPI-184_S18_L003_R1_001	27.5%	28%	101 bp	27%	21.2
EPI-184_S18_L003_R2_001	30.5%	29%	101 bp	18%	21.2
EPI-185_S19_L003_R1_001	33.7%	29%	101 bp	27%	11.3
EPI-185_S19_L003_R2_001	34.7%	29%	101 bp	18%	11.3
EPI-187_S20_L003_R1_001	36.1%	30%	101 bp	27%	26.2
EPI-187_S20_L003_R2_001	39.4%	31%	101 bp	27%	26.2
EPI-188_S21_L003_R1_001	33.8%	31%	101 bp	45%	24.2
EPI-188_S21_L003_R2_001	35.3%	32%	101 bp	36%	24.2
EPI-193_S22_L003_R1_001	35.4%	32%	101 bp	36%	32.6
EPI-193_S22_L003_R2_001	37.8%	33%	101 bp	27%	32.6
EPI-194_S23_L003_R1_001	25.6%	27%	101 bp	27%	28.2
EPI-194_S23_L003_R2_001	30.7%	27%	101 bp	27%	28.2
EPI-199_S24_L003_R1_001	36.4%	31%	101 bp	36%	18.0
EPI-199_S24_L003_R2_001	38.0%	32%	101 bp	18%	18.0
EPI-200_S25_L003_R1_001	33.4%	30%	101 bp	36%	27.9
EPI-200_S25_L003_R2_001	36.9%	31%	101 bp	27%	27.9
EPI-205_S26_L004_R1_001	51.0%	35%	101 bp	45%	26.6
EPI-205_S26_L004_R2_001	50.3%	37%	101 bp	45%	26.6
EPI-206_S27_L004_R1_001	54.3%	36%	101 bp	45%	36.7
EPI-206_S27_L004_R2_001	54.1%	37%	101 bp	45%	36.7
EPI-208_S28_L004_R1_001	41.7%	34%	101 bp	36%	39.1
EPI-208_S28_L004_R2_001	41.5%	35%	101 bp	36%	39.1
EPI-209_S29_L004_R1_001	32.5%	29%	101 bp	18%	31.4
EPI-209_S29_L004_R2_001	36.8%	30%	101 bp	18%	31.4
EPI-214_S30_L004_R1_001	29.3%	29%	101 bp	18%	30.6
EPI-214_S30_L004_R2_001	30.8%	29%	101 bp	18%	30.6
EPI-215_S31_L004_R1_001	36.1%	31%	101 bp	27%	24.2
EPI-215_S31_L004_R2_001	38.9%	31%	101 bp	27%	24.2
EPI-220_S32_L004_R1_001	39.4%	30%	101 bp	18%	17.8
EPI-220_S32_L004_R2_001	40.2%	31%	101 bp	18%	17.8
EPI-221_S33_L004_R1_001	50.0%	34%	101 bp	45%	24.2
EPI-221_S33_L004_R2_001	50.1%	35%	101 bp	45%	24.2
EPI-226_S34_L004_R1_001	29.8%	28%	101 bp	18%	11.6
EPI-226_S34_L004_R2_001	31.5%	29%	101 bp	18%	11.6
EPI-227_S35_L004_R1_001	36.3%	30%	101 bp	27%	15.9
EPI-227_S35_L004_R2_001	37.6%	31%	101 bp	27%	15.9
EPI-229_S36_L004_R1_001	29.4%	30%	101 bp	18%	20.9
EPI-229_S36_L004_R2_001	31.7%	30%	101 bp	18%	20.9
EPI-230_S37_L004_R1_001	39.5%	30%	101 bp	18%	32.4
EPI-230_S37_L004_R2_001	40.6%	31%	101 bp	18%	32.4
EPI-41_S38_L005_R1_001	36.3%	29%	101 bp	18%	25.8
EPI-41_S38_L005_R2_001	36.6%	30%	101 bp	18%	25.8
EPI-42_S39_L005_R1_001	33.6%	29%	101 bp	18%	30.0
EPI-42_S39_L005_R2_001	38.1%	29%	101 bp	27%	30.0
EPI-43_S40_L005_R1_001	47.9%	32%	101 bp	27%	29.4
EPI-43_S40_L005_R2_001	47.5%	33%	101 bp	27%	29.4
EPI-44_S41_L005_R1_001	73.0%	39%	101 bp	55%	38.9
EPI-44_S41_L005_R2_001	68.1%	41%	101 bp	55%	38.9

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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.

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.

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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 (101bp).

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.

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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.

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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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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