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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.

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Report generated on 2017-11-23, 22:11 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HW23FBCXY/2

General Statistics

Showing ⁵⁸/₅₈ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
HW23FBCXY_l02n01_s2_137_rr.351000000a9207	91.1%	41%	151 bp	25%	7.6
HW23FBCXY_l02n01_s2_291_rr.351000000a9214	80.4%	43%	151 bp	25%	8.3
HW23FBCXY_l02n01_s2_297_rr.351000000a9221	94.7%	40%	151 bp	17%	6.9
HW23FBCXY_l02n01_s2_310_rr.351000000a923e	78.4%	43%	151 bp	25%	6.6
HW23FBCXY_l02n01_s2_323_rr.351000000a924b	69.5%	44%	151 bp	25%	8.2
HW23FBCXY_l02n01_s2_325_rr.351000000a9258	79.5%	43%	151 bp	25%	7.2
HW23FBCXY_l02n01_s2_328_rr.351000000a9264	91.8%	40%	151 bp	25%	6.8
HW23FBCXY_l02n01_s2_337_rr.351000000a9271	71.5%	44%	151 bp	25%	7.8
HW23FBCXY_l02n01_s2_338_rr.351000000a928e	93.4%	40%	151 bp	25%	5.5
HW23FBCXY_l02n01_s2_361_rr.351000000a929b	92.6%	40%	151 bp	25%	5.2
HW23FBCXY_l02n01_s2_363_rr.351000000a92a8	90.7%	42%	151 bp	25%	6.6
HW23FBCXY_l02n01_s2_379_rr.351000000a92b4	95.5%	40%	151 bp	25%	4.0
HW23FBCXY_l02n01_s2_394_rr.351000000a92c1	95.7%	41%	151 bp	25%	7.5
HW23FBCXY_l02n01_s2_395_rr.351000000a92de	93.0%	40%	151 bp	25%	4.5
HW23FBCXY_l02n01_s2_412_rr.351000000a92f8	94.6%	40%	151 bp	25%	5.4
HW23FBCXY_l02n01_s2_425_rr.351000000a9306	94.1%	43%	151 bp	33%	6.4
HW23FBCXY_l02n01_s2_428_rr.351000000a9313	76.3%	46%	151 bp	25%	5.5
HW23FBCXY_l02n01_s2_extraction_neg_ctrl_rr.351000000a933d	87.1%	41%	151 bp	25%	0.5
HW23FBCXY_l02n01_s2_lp_ctrl_rr.351000000a93dd	7.2%	44%	151 bp	25%	0.0
HW23FBCXY_l02n01_s2_ny238_rr.351000000a93c0	95.3%	47%	151 bp	25%	2.7
HW23FBCXY_l02n01_s2_pr8-vww_1-100_rr.351000000a93a7	95.9%	40%	151 bp	25%	5.9
HW23FBCXY_l02n01_s2_pr8-vww_1-10_rr.351000000a939a	95.3%	40%	151 bp	17%	5.3
HW23FBCXY_l02n01_s2_pr8-vww_1-1_rr.351000000a9370	95.2%	42%	151 bp	17%	6.1
HW23FBCXY_l02n01_s2_pr8-vww_1-5_rr.351000000a938d	95.6%	41%	151 bp	17%	6.6
HW23FBCXY_l02n01_s2_pr8-vww_10-1_rr.351000000a9357	94.0%	44%	151 bp	17%	2.7
HW23FBCXY_l02n01_s2_pr8-vww_100-1_rr.351000000a934a	95.6%	44%	151 bp	25%	5.1
HW23FBCXY_l02n01_s2_pr8-vww_5-1_rr.351000000a9363	95.4%	43%	151 bp	17%	6.5
HW23FBCXY_l02n01_s2_pr8_cw_rr.351000000a93b3	96.3%	44%	151 bp	25%	6.6
HW23FBCXY_l02n01_s2_vww_10e3_p1_rr.351000000a92eb	96.6%	44%	151 bp	25%	7.3
HW23FBCXY_l02n02_s2_137_rr.352000000a9204	88.8%	41%	151 bp	33%	7.6
HW23FBCXY_l02n02_s2_291_rr.352000000a9211	78.0%	43%	151 bp	33%	8.3
HW23FBCXY_l02n02_s2_297_rr.352000000a922e	92.2%	40%	151 bp	33%	6.9
HW23FBCXY_l02n02_s2_310_rr.352000000a923b	74.7%	43%	151 bp	33%	6.6
HW23FBCXY_l02n02_s2_323_rr.352000000a9248	67.5%	44%	151 bp	33%	8.2
HW23FBCXY_l02n02_s2_325_rr.352000000a9255	76.3%	43%	151 bp	33%	7.2
HW23FBCXY_l02n02_s2_328_rr.352000000a9261	88.7%	40%	151 bp	33%	6.8
HW23FBCXY_l02n02_s2_337_rr.352000000a927e	69.5%	44%	151 bp	33%	7.8
HW23FBCXY_l02n02_s2_338_rr.352000000a928b	89.9%	40%	151 bp	25%	5.5
HW23FBCXY_l02n02_s2_361_rr.352000000a9298	89.0%	40%	151 bp	33%	5.2
HW23FBCXY_l02n02_s2_363_rr.352000000a92a5	89.3%	42%	151 bp	33%	6.6
HW23FBCXY_l02n02_s2_379_rr.352000000a92b1	90.1%	40%	151 bp	33%	4.0
HW23FBCXY_l02n02_s2_394_rr.352000000a92ce	93.9%	41%	151 bp	33%	7.5
HW23FBCXY_l02n02_s2_395_rr.352000000a92db	88.7%	40%	151 bp	33%	4.5
HW23FBCXY_l02n02_s2_412_rr.352000000a92f5	90.9%	40%	151 bp	33%	5.4
HW23FBCXY_l02n02_s2_425_rr.352000000a9303	89.2%	43%	151 bp	42%	6.4
HW23FBCXY_l02n02_s2_428_rr.352000000a9310	73.5%	46%	151 bp	33%	5.5
HW23FBCXY_l02n02_s2_extraction_neg_ctrl_rr.352000000a933a	86.6%	41%	151 bp	42%	0.5
HW23FBCXY_l02n02_s2_lp_ctrl_rr.352000000a93da	2.8%	44%	151 bp	17%	0.0
HW23FBCXY_l02n02_s2_ny238_rr.352000000a93cd	88.8%	47%	151 bp	42%	2.7
HW23FBCXY_l02n02_s2_pr8-vww_1-100_rr.352000000a93a4	92.8%	40%	151 bp	33%	5.9
HW23FBCXY_l02n02_s2_pr8-vww_1-10_rr.352000000a9397	91.1%	40%	151 bp	33%	5.3
HW23FBCXY_l02n02_s2_pr8-vww_1-1_rr.352000000a937d	90.7%	42%	151 bp	33%	6.1
HW23FBCXY_l02n02_s2_pr8-vww_1-5_rr.352000000a938a	91.2%	41%	151 bp	33%	6.6
HW23FBCXY_l02n02_s2_pr8-vww_10-1_rr.352000000a9354	88.8%	44%	151 bp	33%	2.7
HW23FBCXY_l02n02_s2_pr8-vww_100-1_rr.352000000a9347	90.1%	44%	151 bp	33%	5.1
HW23FBCXY_l02n02_s2_pr8-vww_5-1_rr.352000000a9360	91.3%	43%	151 bp	33%	6.5
HW23FBCXY_l02n02_s2_pr8_cw_rr.352000000a93b0	93.8%	44%	151 bp	33%	6.6
HW23FBCXY_l02n02_s2_vww_10e3_p1_rr.352000000a92e8	95.1%	44%	151 bp	25%	7.3

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

Lane Statistics

Showing ¹/₁ rows and ⁴/₄ columns.

Lane	Total # of Single-End Reads	Total # PF Reads	Undetermined	% PhiX Aligned
2.0	180599860	172497159	4.0	2.0

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

Sort	Column	Description	ID	Scale
\|\|	Total # of Single-End Reads	Total # of Single-End Reads	`Total # of Single-End Reads`	None
\|\|	Total # PF Reads	Total # PF Reads	`Total # PF Reads`	None
\|\|	Undetermined	Undetermined	`Undetermined`	None
\|\|	% PhiX Aligned	% PhiX Aligned	`% PhiX Aligned`	None

Lane 2 Demultiplexing Report

Lane 2 Demultiplexing Report
Total Read Count: Total number of PF (Passing Filter) reads in this library.
Portion: The proportion of reads that represent the individual library in the entire Library Pool.
Perfect: The percentage of reads in this library which have a barcode perfectly matching the barcode specified in TuboWeb. The remainder of reads have mismatches upto the max number of mismatches specified in TuboWeb (Allowed barcode mismatch option in your Library Pool).

Showing ²⁹/₂₉ rows and ³/₃ columns.

Library	Total Read Count	Portion (%)	Perfect (%)
s2_310_rr	6595791	4.0	97.4
s2_323_rr	8240621	5.0	97.8
s2_361_rr	5228559	3.2	96.9
s2_pr8-vww_5-1_rr	6522090	3.9	97.5
s2_extraction_neg_ctrl_rr	451260	0.3	97.1
s2_vww_10e3_p1_rr	7299101	4.4	97.2
s2_pr8_cw_rr	6647585	4.0	97.2
s2_379_rr	4007680	2.4	96.6
s2_pr8-vww_100-1_rr	5145560	3.1	97.0
s2_pr8-vww_1-100_rr	5852777	3.5	97.2
s2_428_rr	5535549	3.3	97.4
s2_395_rr	4477045	2.7	97.0
s2_338_rr	5522606	3.3	97.0
s2_394_rr	7531394	4.5	97.2
s2_297_rr	6915188	4.2	97.8
s2_pr8-vww_1-10_rr	5262659	3.2	97.1
s2_291_rr	8276135	5.0	97.7
s2_lp_ctrl_rr	3068	0.0	38.3
s2_337_rr	7808899	4.7	97.6
s2_pr8-vww_1-5_rr	6601378	4.0	97.3
s2_412_rr	5440985	3.3	96.8
s2_363_rr	6554125	4.0	97.0
s2_328_rr	6774962	4.1	97.9
s2_pr8-vww_10-1_rr	2741820	1.7	97.3
s2_137_rr	7648645	4.6	97.8
s2_425_rr	6372173	3.9	97.5
s2_pr8-vww_1-1_rr	6094072	3.7	97.6
s2_ny238_rr	2738658	1.7	96.6
s2_325_rr	7222447	4.4	97.7

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

Sort	Column	Description	ID	Scale
\|\|	Total Read Count	Total Read Count	`Total Read Count`	None
\|\|	Portion (%)	Portion (%)	`Portion (%)`	None
\|\|	Perfect (%)	Perfect (%)	`Perfect (%)`	None

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.

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.

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.

Per Base N Content

The percentage of base calls at each position for which an N was called. See the FastQC help.

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.

Overrepresented sequences

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

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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Lane 2 Demultiplexing Report

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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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