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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 1.0.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 2017-09-18, 09:09 based on data in: /Volumes/Alanine/wd/17-09-15

General Statistics

Showing ¹²⁸/₁₂₈ rows and ⁴/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
Geoduck-ctenidia-RNA-1_S3_L001_R1_001	33.9%	38%	145	33%	0.0
Geoduck-ctenidia-RNA-1_S3_L001_R2_001	34.8%	37%	145	17%	0.0
Geoduck-ctenidia-RNA-2_S11_L002_R1_001	14.5%	40%	146	25%	0.0
Geoduck-ctenidia-RNA-2_S11_L002_R2_001	16.0%	38%	146	33%	0.0
Geoduck-ctenidia-RNA-3_S19_L003_R1_001	21.1%	46%	147	33%	0.0
Geoduck-ctenidia-RNA-3_S19_L003_R2_001	20.9%	45%	146	42%	0.0
Geoduck-ctenidia-RNA-4_S27_L004_R1_001	13.9%	37%	145	17%	0.0
Geoduck-ctenidia-RNA-4_S27_L004_R2_001	14.5%	37%	145	17%	0.0
Geoduck-ctenidia-RNA-5_S35_L005_R1_001	27.7%	36%	144	17%	1.0
Geoduck-ctenidia-RNA-5_S35_L005_R2_001	28.7%	36%	144	17%	1.0
Geoduck-ctenidia-RNA-6_S43_L006_R1_001	70.6%	36%	145	33%	58.5
Geoduck-ctenidia-RNA-6_S43_L006_R2_001	73.7%	37%	145	25%	58.5
Geoduck-ctenidia-RNA-7_S51_L007_R1_001	18.5%	40%	145	25%	0.0
Geoduck-ctenidia-RNA-7_S51_L007_R2_001	19.2%	39%	145	17%	0.0
Geoduck-ctenidia-RNA-8_S59_L008_R1_001	54.1%	38%	145	33%	0.0
Geoduck-ctenidia-RNA-8_S59_L008_R2_001	56.0%	38%	145	33%	0.0
Geoduck-gonad-RNA-1_S1_L001_R1_001	27.9%	52%	148	42%	0.0
Geoduck-gonad-RNA-1_S1_L001_R2_001	24.9%	51%	148	50%	0.0
Geoduck-gonad-RNA-2_S9_L002_R1_001	16.5%	50%	150	50%	0.0
Geoduck-gonad-RNA-2_S9_L002_R2_001	11.4%	49%	149	50%	0.0
Geoduck-gonad-RNA-3_S17_L003_R1_001	8.0%	63%	149	50%	0.0
Geoduck-gonad-RNA-3_S17_L003_R2_001	6.1%	62%	149	42%	0.0
Geoduck-gonad-RNA-4_S25_L004_R1_001	11.3%	60%	149	42%	0.0
Geoduck-gonad-RNA-4_S25_L004_R2_001	8.1%	58%	149	50%	0.0
Geoduck-gonad-RNA-5_S33_L005_R1_001	6.2%	62%	150	50%	0.0
Geoduck-gonad-RNA-5_S33_L005_R2_001	5.6%	60%	151	50%	0.0
Geoduck-gonad-RNA-6_S41_L006_R1_001	13.9%	72%	150	50%	0.0
Geoduck-gonad-RNA-6_S41_L006_R2_001	5.6%	67%	150	42%	0.0
Geoduck-gonad-RNA-7_S49_L007_R1_001	43.3%	44%	145	50%	0.0
Geoduck-gonad-RNA-7_S49_L007_R2_001	41.5%	42%	145	50%	0.0
Geoduck-gonad-RNA-8_S57_L008_R1_001	80.5%	37%	145	25%	55.7
Geoduck-gonad-RNA-8_S57_L008_R2_001	87.9%	37%	145	25%	55.7
Geoduck-heart-RNA-1_S2_L001_R1_001	58.3%	39%	145	33%	0.0
Geoduck-heart-RNA-1_S2_L001_R2_001	62.3%	39%	145	33%	0.0
Geoduck-heart-RNA-2_S10_L002_R1_001	7.0%	40%	147	42%	0.0
Geoduck-heart-RNA-2_S10_L002_R2_001	6.9%	38%	146	33%	0.0
Geoduck-heart-RNA-3_S18_L003_R1_001	36.1%	37%	144	17%	0.0
Geoduck-heart-RNA-3_S18_L003_R2_001	42.5%	37%	144	17%	0.0
Geoduck-heart-RNA-4_S26_L004_R1_001	3.9%	38%	146	17%	0.0
Geoduck-heart-RNA-4_S26_L004_R2_001	4.1%	39%	146	17%	0.0
Geoduck-heart-RNA-5_S34_L005_R1_001	11.2%	38%	147	25%	0.1
Geoduck-heart-RNA-5_S34_L005_R2_001	14.9%	39%	146	17%	0.1
Geoduck-heart-RNA-6_S42_L006_R1_001	25.4%	43%	144	33%	0.0
Geoduck-heart-RNA-6_S42_L006_R2_001	25.6%	42%	143	17%	0.0
Geoduck-heart-RNA-7_S50_L007_R1_001	75.7%	38%	143	25%	104.6
Geoduck-heart-RNA-7_S50_L007_R2_001	77.1%	38%	143	25%	104.6
Geoduck-heart-RNA-8_S58_L008_R1_001	34.9%	38%	144	8%	0.0
Geoduck-heart-RNA-8_S58_L008_R2_001	35.5%	38%	144	25%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-115-1_S4_L001_R1_001	23.4%	50%	147	33%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-115-1_S4_L001_R2_001	17.9%	48%	147	33%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-115-2_S12_L002_R1_001	6.2%	46%	150	58%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-115-2_S12_L002_R2_001	3.8%	40%	150	50%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-115-3_S20_L003_R1_001	22.0%	48%	149	33%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-115-3_S20_L003_R2_001	14.2%	46%	148	50%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-115-4_S28_L004_R1_001	26.7%	38%	146	17%	1.4
Geoduck-juvenile-OA-exposure-RNA-EPI-115-4_S28_L004_R2_001	27.8%	39%	145	17%	1.4
Geoduck-juvenile-OA-exposure-RNA-EPI-115-5_S36_L005_R1_001	73.9%	38%	145	25%	78.5
Geoduck-juvenile-OA-exposure-RNA-EPI-115-5_S36_L005_R2_001	83.8%	39%	145	25%	78.5
Geoduck-juvenile-OA-exposure-RNA-EPI-115-6_S44_L006_R1_001	28.4%	49%	146	33%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-115-6_S44_L006_R2_001	22.0%	47%	146	42%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-115-7_S52_L007_R1_001	15.0%	41%	148	17%	0.1
Geoduck-juvenile-OA-exposure-RNA-EPI-115-7_S52_L007_R2_001	17.1%	38%	146	17%	0.1
Geoduck-juvenile-OA-exposure-RNA-EPI-115-8_S60_L008_R1_001	54.9%	45%	139	50%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-115-8_S60_L008_R2_001	48.4%	46%	140	33%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-116-1_S5_L001_R1_001	52.4%	40%	146	33%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-116-1_S5_L001_R2_001	55.9%	40%	146	33%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-116-2_S13_L002_R1_001	8.4%	45%	148	33%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-116-2_S13_L002_R2_001	8.0%	41%	147	42%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-116-3_S21_L003_R1_001	17.5%	38%	142	33%	0.6
Geoduck-juvenile-OA-exposure-RNA-EPI-116-3_S21_L003_R2_001	18.6%	38%	142	25%	0.6
Geoduck-juvenile-OA-exposure-RNA-EPI-116-4_S29_L004_R1_001	63.6%	37%	145	25%	90.8
Geoduck-juvenile-OA-exposure-RNA-EPI-116-4_S29_L004_R2_001	66.8%	38%	145	25%	90.8
Geoduck-juvenile-OA-exposure-RNA-EPI-116-5_S37_L005_R1_001	45.1%	39%	146	17%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-116-5_S37_L005_R2_001	49.9%	39%	146	17%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-116-6_S45_L006_R1_001	28.8%	52%	148	42%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-116-6_S45_L006_R2_001	25.4%	49%	148	50%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-116-7_S53_L007_R1_001	14.9%	40%	147	17%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-116-7_S53_L007_R2_001	10.5%	39%	146	33%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-116-8_S61_L008_R1_001	82.4%	37%	146	25%	0.0
Geoduck-juvenile-OA-exposure-RNA-EPI-116-8_S61_L008_R2_001	84.5%	38%	146	25%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-1_S6_L001_R1_001	25.3%	59%	149	42%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-1_S6_L001_R2_001	15.8%	57%	148	42%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-2_S14_L002_R1_001	38.6%	36%	143	17%	2.1
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-2_S14_L002_R2_001	37.7%	36%	143	17%	2.1
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-3_S22_L003_R1_001	68.3%	36%	143	33%	60.8
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-3_S22_L003_R2_001	76.0%	37%	143	25%	60.8
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-4_S30_L004_R1_001	14.0%	40%	146	25%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-4_S30_L004_R2_001	16.0%	40%	146	8%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-5_S38_L005_R1_001	16.2%	46%	149	33%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-5_S38_L005_R2_001	15.1%	44%	147	42%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-6_S46_L006_R1_001	12.3%	46%	146	33%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-6_S46_L006_R2_001	8.3%	44%	146	42%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-7_S54_L007_R1_001	33.1%	38%	143	8%	0.1
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-7_S54_L007_R2_001	33.8%	38%	143	8%	0.1
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-8_S62_L008_R1_001	42.3%	51%	149	33%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-8_S62_L008_R2_001	43.1%	51%	148	42%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-1_S7_L001_R1_001	42.3%	38%	145	17%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-1_S7_L001_R2_001	47.6%	39%	145	25%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-2_S15_L002_R1_001	67.1%	36%	144	25%	93.9
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-2_S15_L002_R2_001	68.7%	37%	144	25%	93.9
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-3_S23_L003_R1_001	16.8%	45%	149	42%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-3_S23_L003_R2_001	14.5%	44%	147	42%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-4_S31_L004_R1_001	8.7%	55%	149	50%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-4_S31_L004_R2_001	5.2%	51%	149	50%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-5_S39_L005_R1_001	40.1%	44%	148	33%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-5_S39_L005_R2_001	46.6%	43%	148	33%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-6_S47_L006_R1_001	35.0%	57%	148	50%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-6_S47_L006_R2_001	26.1%	53%	147	50%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-7_S55_L007_R1_001	5.2%	42%	146	33%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-7_S55_L007_R2_001	4.5%	41%	145	25%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-8_S63_L008_R1_001	13.4%	40%	146	33%	0.0
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-8_S63_L008_R2_001	14.1%	39%	145	33%	0.0
Geoduck-larvae-day5-RNA-EPI-99-1_S8_L001_R1_001	71.8%	38%	145	25%	61.3
Geoduck-larvae-day5-RNA-EPI-99-1_S8_L001_R2_001	78.9%	38%	145	25%	61.3
Geoduck-larvae-day5-RNA-EPI-99-2_S16_L002_R1_001	14.7%	53%	148	42%	0.0
Geoduck-larvae-day5-RNA-EPI-99-2_S16_L002_R2_001	11.8%	51%	149	50%	0.0
Geoduck-larvae-day5-RNA-EPI-99-3_S24_L003_R1_001	23.6%	63%	150	58%	0.0
Geoduck-larvae-day5-RNA-EPI-99-3_S24_L003_R2_001	14.9%	59%	149	50%	0.0
Geoduck-larvae-day5-RNA-EPI-99-4_S32_L004_R1_001	10.4%	48%	146	33%	0.0
Geoduck-larvae-day5-RNA-EPI-99-4_S32_L004_R2_001	8.7%	46%	146	42%	0.0
Geoduck-larvae-day5-RNA-EPI-99-5_S40_L005_R1_001	64.8%	39%	145	17%	0.0
Geoduck-larvae-day5-RNA-EPI-99-5_S40_L005_R2_001	72.6%	39%	145	17%	0.0
Geoduck-larvae-day5-RNA-EPI-99-6_S48_L006_R1_001	24.9%	74%	150	50%	0.0
Geoduck-larvae-day5-RNA-EPI-99-6_S48_L006_R2_001	3.7%	66%	149	50%	0.0
Geoduck-larvae-day5-RNA-EPI-99-7_S56_L007_R1_001	6.2%	52%	149	50%	0.0
Geoduck-larvae-day5-RNA-EPI-99-7_S56_L007_R2_001	3.3%	48%	149	42%	0.0
Geoduck-larvae-day5-RNA-EPI-99-8_S64_L008_R1_001	28.1%	53%	146	42%	0.0
Geoduck-larvae-day5-RNA-EPI-99-8_S64_L008_R2_001	25.4%	51%	146	42%	0.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

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 heatmap row to see a line plot for that dataset.

rollover for sample name

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Sequence Length Distribution

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

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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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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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