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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.

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Report generated on 2018-01-16, 08:01 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/H5TH7BCX2/1

General Statistics

Showing ²⁶/₂₆ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
H5TH7BCX2_l01n01_gal-ssb_gal_doxrap-1.351000000b0e63	67.5%	46%	51 bp	50%	12.0
H5TH7BCX2_l01n01_gal-ssb_gal_doxrap-2.351000000b0e8d	69.2%	46%	51 bp	50%	11.7
H5TH7BCX2_l01n01_gal-ssb_gal_doxrap-3.351000000b0ea7	62.9%	42%	51 bp	42%	12.4
H5TH7BCX2_l01n01_gal-ssb_glu_doxrap-1.351000000b0ec0	83.4%	44%	51 bp	42%	13.9
H5TH7BCX2_l01n01_gal-ssb_glu_doxrap-2.351000000b0eea	77.5%	43%	51 bp	42%	9.7
H5TH7BCX2_l01n01_gal-ssb_glu_doxrap-3.351000000b0ef7	15.8%	45%	51 bp	17%	0.0
H5TH7BCX2_l01n01_gal-ssb_glu_doxrap-4.351000000b0f12	17.5%	43%	51 bp	25%	0.0
H5TH7BCX2_l01n01_wt-1.351000000b0d9b	51.1%	41%	51 bp	42%	11.4
H5TH7BCX2_l01n01_wt-2.351000000b0db4	47.1%	41%	51 bp	33%	8.6
H5TH7BCX2_l01n01_wt-3.351000000b0deb	46.7%	42%	51 bp	25%	7.5
H5TH7BCX2_l01n01_wt-hu-1.351000000b0e06	45.4%	40%	51 bp	17%	4.4
H5TH7BCX2_l01n01_wt-hu-2.351000000b0e13	45.5%	42%	51 bp	33%	2.7
H5TH7BCX2_l01n01_wt-hu-3.351000000b0e3d	62.0%	40%	51 bp	25%	17.2
H5TH7BCX2_l01n02_gal-ssb_gal_doxrap-1.352000000b0e60	56.3%	47%	51 bp	50%	12.0
H5TH7BCX2_l01n02_gal-ssb_gal_doxrap-2.352000000b0e8a	60.2%	48%	51 bp	50%	11.7
H5TH7BCX2_l01n02_gal-ssb_gal_doxrap-3.352000000b0ea4	54.5%	43%	51 bp	50%	12.4
H5TH7BCX2_l01n02_gal-ssb_glu_doxrap-1.352000000b0ecd	74.4%	45%	51 bp	50%	13.9
H5TH7BCX2_l01n02_gal-ssb_glu_doxrap-2.352000000b0ee7	66.7%	44%	51 bp	50%	9.7
H5TH7BCX2_l01n02_gal-ssb_glu_doxrap-3.352000000b0ef4	13.6%	45%	51 bp	8%	0.0
H5TH7BCX2_l01n02_gal-ssb_glu_doxrap-4.352000000b0f1f	10.5%	45%	51 bp	8%	0.0
H5TH7BCX2_l01n02_wt-1.352000000b0d98	42.6%	42%	51 bp	25%	11.4
H5TH7BCX2_l01n02_wt-2.352000000b0db1	39.5%	41%	51 bp	25%	8.6
H5TH7BCX2_l01n02_wt-3.352000000b0de8	38.9%	42%	51 bp	33%	7.5
H5TH7BCX2_l01n02_wt-hu-1.352000000b0e03	38.2%	41%	51 bp	25%	4.4
H5TH7BCX2_l01n02_wt-hu-2.352000000b0e10	38.0%	43%	51 bp	42%	2.7
H5TH7BCX2_l01n02_wt-hu-3.352000000b0e3a	53.9%	41%	51 bp	33%	17.2

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
1.0	121498564	116794120	4.5	2.2

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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 1 Demultiplexing Report

Lane 1 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 ¹³/₁₃ rows and ³/₃ columns.

Library	Total Read Count	Portion (%)	Perfect (%)
gal-ssb_glu_doxrap-3	5762	0.0	6.5
gal-ssb_gal_doxrap-3	12419293	11.1	97.3
gal-ssb_gal_doxrap-2	11731792	10.5	96.4
wt-2	8598248	7.7	97.9
wt-hu-2	2687568	2.4	97.0
wt-1	11414441	10.2	96.7
gal-ssb_gal_doxrap-1	12049509	10.8	96.2
gal-ssb_glu_doxrap-1	13852477	12.4	97.6
gal-ssb_glu_doxrap-2	9730794	8.7	97.5
wt-3	7548181	6.8	97.1
wt-hu-3	17164432	15.4	98.5
wt-hu-1	4370130	3.9	97.7
gal-ssb_glu_doxrap-4	26078	0.0	3.3

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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 (51bp).

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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About MultiQC

General Statistics

General Statistics: Columns

Lane Statistics

Table Ikdb: Columns

Lane 1 Demultiplexing Report

Table Kafh: Columns

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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