MultiQC Report

Toolbox

MultiQC Toolbox

Highlight Samples

Regex mode off

Rename Samples

Click here for bulk input.

Paste two columns of a tab-delimited table here (eg. from Excel).

First column should be the old name, second column the new name.

Regex mode off

Show / Hide Samples

Regex mode off

Export Plots

Images
Data

Aspect ratio

Plot scaling

Download the raw data used to create the plots in this report below:

Format:

Note that additional data was saved in multiqc_data when this report was generated.

Choose Plots

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

Save Settings

You can save the toolbox settings for this report to the browser.

Load Settings

Choose a saved report profile from the dropdown box below:

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.

Loading report..

Report generated on 2018-04-18, 14:04 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H2CYMAFXY/merged

General Statistics

Showing ⁸²/₈₂ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
H2CYMAFXY_n01_284_nextera	88.4%	43%	150 bp	33%	3.7
H2CYMAFXY_n01_284_sispa	83.7%	42%	150 bp	33%	0.7
H2CYMAFXY_n01_297_nextera	90.1%	41%	150 bp	33%	2.9
H2CYMAFXY_n01_297_sispa	75.3%	41%	150 bp	33%	0.9
H2CYMAFXY_n01_302_nextera	77.9%	44%	150 bp	33%	2.8
H2CYMAFXY_n01_302_sispa	68.6%	42%	150 bp	33%	0.6
H2CYMAFXY_n01_310_nextera	78.3%	44%	150 bp	33%	3.4
H2CYMAFXY_n01_310_sispa	79.9%	48%	150 bp	42%	0.7
H2CYMAFXY_n01_328_nextera	85.5%	42%	150 bp	33%	3.0
H2CYMAFXY_n01_328_sispa	77.2%	42%	150 bp	33%	0.6
H2CYMAFXY_n01_337_nextera	65.0%	45%	150 bp	42%	3.2
H2CYMAFXY_n01_337_sispa	67.8%	43%	150 bp	42%	0.7
H2CYMAFXY_n01_338_nextera	89.6%	43%	150 bp	25%	3.5
H2CYMAFXY_n01_338_sispa	78.3%	43%	150 bp	33%	0.7
H2CYMAFXY_n01_346_nextera	77.5%	44%	150 bp	33%	3.7
H2CYMAFXY_n01_346_sispa	73.4%	45%	150 bp	33%	0.8
H2CYMAFXY_n01_361_nextera	87.4%	41%	150 bp	33%	2.7
H2CYMAFXY_n01_361_sispa	84.1%	43%	150 bp	33%	0.8
H2CYMAFXY_n01_379_nextera	92.2%	41%	150 bp	33%	2.6
H2CYMAFXY_n01_379_sispa	86.0%	42%	150 bp	33%	0.7
H2CYMAFXY_n01_394_nextera	90.9%	44%	150 bp	42%	3.2
H2CYMAFXY_n01_394_sispa	87.1%	45%	150 bp	42%	0.5
H2CYMAFXY_n01_412_nextera	88.6%	42%	150 bp	33%	3.0
H2CYMAFXY_n01_412_sispa	79.4%	44%	150 bp	42%	0.9
H2CYMAFXY_n01_428_nextera	70.4%	45%	150 bp	42%	3.2
H2CYMAFXY_n01_428_sispa	74.5%	44%	150 bp	33%	0.6
H2CYMAFXY_n01_460_nextera	90.4%	44%	150 bp	33%	4.7
H2CYMAFXY_n01_460_sispa	89.9%	47%	150 bp	42%	1.5
H2CYMAFXY_n01_463_nextera	86.3%	41%	150 bp	33%	2.0
H2CYMAFXY_n01_463_sispa	88.3%	43%	150 bp	33%	0.8
H2CYMAFXY_n01_cal-09_nextera	92.9%	44%	150 bp	25%	3.3
H2CYMAFXY_n01_cal-09_sispa	87.6%	45%	150 bp	33%	0.8
H2CYMAFXY_n01_lp_negative_control_nextera	0.0%	47%	150 bp	33%	0.0
H2CYMAFXY_n01_lp_negative_control_sispa	93.3%	71%	150 bp	42%	0.0
H2CYMAFXY_n01_ny238_plasmid_mix_nextera	93.0%	47%	150 bp	25%	1.8
H2CYMAFXY_n01_ny238_plasmid_mix_sispa	88.8%	46%	150 bp	33%	0.7
H2CYMAFXY_n01_smart_methods_extraction_control_nextera	92.9%	46%	150 bp	42%	0.9
H2CYMAFXY_n01_smart_methods_extraction_control_sispa	91.2%	43%	150 bp	42%	0.8
H2CYMAFXY_n01_smart_methods_pcr_control_sispa	66.0%	69%	150 bp	42%	0.0
H2CYMAFXY_n01_smart_pool1_sispa	85.0%	44%	150 bp	42%	16.2
H2CYMAFXY_n01_smart_pool2_sispa	85.3%	44%	150 bp	42%	16.6
H2CYMAFXY_n02_284_nextera	85.3%	43%	150 bp	33%	3.7
H2CYMAFXY_n02_284_sispa	81.9%	42%	150 bp	33%	0.7
H2CYMAFXY_n02_297_nextera	87.7%	41%	150 bp	33%	2.9
H2CYMAFXY_n02_297_sispa	73.5%	42%	150 bp	33%	0.9
H2CYMAFXY_n02_302_nextera	74.8%	43%	150 bp	33%	2.8
H2CYMAFXY_n02_302_sispa	67.2%	42%	150 bp	42%	0.6
H2CYMAFXY_n02_310_nextera	75.6%	44%	150 bp	33%	3.4
H2CYMAFXY_n02_310_sispa	79.5%	49%	150 bp	42%	0.7
H2CYMAFXY_n02_328_nextera	82.9%	42%	150 bp	33%	3.0
H2CYMAFXY_n02_328_sispa	75.2%	42%	150 bp	33%	0.6
H2CYMAFXY_n02_337_nextera	63.1%	45%	150 bp	33%	3.2
H2CYMAFXY_n02_337_sispa	67.4%	43%	150 bp	33%	0.7
H2CYMAFXY_n02_338_nextera	87.5%	42%	150 bp	33%	3.5
H2CYMAFXY_n02_338_sispa	76.8%	43%	150 bp	33%	0.7
H2CYMAFXY_n02_346_nextera	75.4%	44%	150 bp	33%	3.7
H2CYMAFXY_n02_346_sispa	71.8%	44%	150 bp	33%	0.8
H2CYMAFXY_n02_361_nextera	84.6%	41%	150 bp	33%	2.7
H2CYMAFXY_n02_361_sispa	82.8%	43%	150 bp	33%	0.8
H2CYMAFXY_n02_379_nextera	90.2%	41%	150 bp	33%	2.6
H2CYMAFXY_n02_379_sispa	84.2%	42%	150 bp	33%	0.7
H2CYMAFXY_n02_394_nextera	88.6%	43%	150 bp	42%	3.2
H2CYMAFXY_n02_394_sispa	85.6%	45%	150 bp	33%	0.5
H2CYMAFXY_n02_412_nextera	85.6%	42%	150 bp	33%	3.0
H2CYMAFXY_n02_412_sispa	79.4%	44%	150 bp	33%	0.9
H2CYMAFXY_n02_428_nextera	68.9%	45%	150 bp	42%	3.2
H2CYMAFXY_n02_428_sispa	75.2%	43%	150 bp	33%	0.6
H2CYMAFXY_n02_460_nextera	88.7%	44%	150 bp	42%	4.7
H2CYMAFXY_n02_460_sispa	89.5%	46%	150 bp	42%	1.5
H2CYMAFXY_n02_463_nextera	84.0%	41%	150 bp	33%	2.0
H2CYMAFXY_n02_463_sispa	87.2%	43%	150 bp	33%	0.8
H2CYMAFXY_n02_cal-09_nextera	90.8%	44%	150 bp	33%	3.3
H2CYMAFXY_n02_cal-09_sispa	85.8%	45%	150 bp	33%	0.8
H2CYMAFXY_n02_lp_negative_control_nextera	8.3%	51%	150 bp	33%	0.0
H2CYMAFXY_n02_lp_negative_control_sispa	14.5%	72%	150 bp	42%	0.0
H2CYMAFXY_n02_ny238_plasmid_mix_nextera	90.2%	46%	150 bp	33%	1.8
H2CYMAFXY_n02_ny238_plasmid_mix_sispa	86.7%	46%	150 bp	33%	0.7
H2CYMAFXY_n02_smart_methods_extraction_control_nextera	91.4%	45%	150 bp	33%	0.9
H2CYMAFXY_n02_smart_methods_extraction_control_sispa	92.0%	43%	150 bp	33%	0.8
H2CYMAFXY_n02_smart_methods_pcr_control_sispa	6.8%	75%	150 bp	42%	0.0
H2CYMAFXY_n02_smart_pool1_sispa	83.8%	44%	150 bp	42%	16.2
H2CYMAFXY_n02_smart_pool2_sispa	84.1%	44%	150 bp	42%	16.6

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

Run Statistics

Showing ¹/₁ rows and ⁴/₄ columns.

Number of Lanes	Total # of Single-End Reads	Total # PF Reads	Undetermined	% PhiX Aligned
4.0	128761577	107913677	7.3	2.3

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

Demultiplexing Report

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 ⁴¹/₄₁ rows and ³/₃ columns.

Library	Total Read Count	Portion (%)	Perfect (%)
297_sispa	930264	0.9	97.7
297_nextera	2863562	2.9	98.7
338_nextera	3547032	3.5	98.9
lp_negative_control_nextera	12.0	0.0	62.5
460_nextera	4715998	4.7	99.0
smart_pool2_sispa	16586537	16.6	98.6
328_sispa	565776	0.6	97.1
lp_negative_control_sispa	4182	0.0	98.3
337_nextera	3159994	3.2	98.8
310_sispa	740014	0.7	96.9
cal-09_sispa	807800	0.8	96.1
361_nextera	2699485	2.7	98.7
cal-09_nextera	3310304	3.3	98.3
302_nextera	2815698	2.8	97.8
338_sispa	687538	0.7	97.3
412_nextera	2975328	3.0	98.7
346_sispa	796052	0.8	98.6
337_sispa	733152	0.7	98.0
smart_methods_extraction_control_sispa	844967	0.8	97.2
463_nextera	1962256	2.0	97.2
346_nextera	3654547	3.7	98.7
428_nextera	3183139	3.2	98.8
361_sispa	842996	0.8	97.8
284_sispa	657503	0.7	95.8
463_sispa	820088	0.8	96.1
394_sispa	546786	0.5	98.3
310_nextera	3381506	3.4	98.8
412_sispa	855516	0.9	98.7
smart_methods_extraction_control_nextera	900297	0.9	98.5
379_sispa	650832	0.7	98.4
460_sispa	1471860	1.5	98.9
ny238_plasmid_mix_nextera	1829872	1.8	98.2
428_sispa	566745	0.6	98.6
379_nextera	2615684	2.6	98.6
284_nextera	3700247	3.7	97.9
smart_pool1_sispa	16224319	16.2	98.7
302_sispa	592781	0.6	95.1
smart_methods_pcr_control_sispa	4919	0.0	98.4
ny238_plasmid_mix_sispa	673657	0.7	96.1
328_nextera	2968522	3.0	98.7
394_nextera	3169882	3.2	98.8

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 (150bp).

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.

Toggle navigation v1.0.dev0

MultiQC Toolbox

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Export Plots

Choose Plots

Save Settings

Load Settings

About MultiQC

General Statistics

General Statistics: Columns

Run Statistics

Table Fpiv: Columns

Demultiplexing Report

Table Hkbl: 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

v1.0.dev0

Highlight Samples

Rename Samples

Show / Hide Samples