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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 2018-04-03, 16:04 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HLFF3BGX5/merged

General Statistics

Showing ⁶⁴/₆₄ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
HLFF3BGX5_n01_eq0	51.0%	41%	75 bp	33%	14.4
HLFF3BGX5_n01_eq1	50.9%	41%	75 bp	33%	15.0
HLFF3BGX5_n01_eq2	54.4%	42%	75 bp	33%	16.5
HLFF3BGX5_n01_eq3	51.8%	42%	75 bp	33%	16.2
HLFF3BGX5_n01_eq4	50.4%	41%	75 bp	25%	12.4
HLFF3BGX5_n01_ew0	44.7%	41%	75 bp	25%	11.2
HLFF3BGX5_n01_ew1	45.4%	40%	75 bp	17%	11.5
HLFF3BGX5_n01_ew2	47.0%	41%	75 bp	25%	15.5
HLFF3BGX5_n01_ew3	47.9%	41%	75 bp	25%	14.2
HLFF3BGX5_n01_ew4	52.8%	41%	75 bp	33%	14.8
HLFF3BGX5_n01_hq0	53.7%	41%	75 bp	33%	15.2
HLFF3BGX5_n01_hq1	50.2%	42%	75 bp	33%	16.1
HLFF3BGX5_n01_hq2	52.6%	41%	75 bp	33%	13.8
HLFF3BGX5_n01_hq3	73.1%	45%	75 bp	25%	16.8
HLFF3BGX5_n01_hq4	59.0%	42%	75 bp	25%	13.3
HLFF3BGX5_n01_hw0	57.9%	42%	75 bp	25%	15.2
HLFF3BGX5_n01_hw1	45.2%	43%	75 bp	25%	17.7
HLFF3BGX5_n01_hw2	32.8%	42%	75 bp	25%	17.6
HLFF3BGX5_n01_hw3	46.6%	43%	75 bp	25%	10.9
HLFF3BGX5_n01_hw4	55.0%	42%	75 bp	33%	15.3
HLFF3BGX5_n01_other_stuff_1	50.8%	39%	75 bp	25%	12.5
HLFF3BGX5_n01_other_stuff_2	53.6%	40%	75 bp	25%	17.2
HLFF3BGX5_n01_sq0	70.0%	44%	75 bp	25%	22.5
HLFF3BGX5_n01_sq1	60.2%	42%	75 bp	25%	17.7
HLFF3BGX5_n01_sq2	54.0%	41%	75 bp	25%	11.8
HLFF3BGX5_n01_sq3	56.5%	42%	75 bp	25%	16.1
HLFF3BGX5_n01_sq4	57.3%	41%	75 bp	25%	12.4
HLFF3BGX5_n01_sw0	48.0%	42%	75 bp	25%	10.9
HLFF3BGX5_n01_sw1	39.8%	42%	75 bp	25%	14.2
HLFF3BGX5_n01_sw2	51.7%	43%	75 bp	33%	16.8
HLFF3BGX5_n01_sw3	54.5%	42%	75 bp	33%	17.3
HLFF3BGX5_n01_sw4	55.5%	46%	75 bp	33%	14.7
HLFF3BGX5_n02_eq0	50.9%	41%	75 bp	33%	14.4
HLFF3BGX5_n02_eq1	49.7%	41%	75 bp	25%	15.0
HLFF3BGX5_n02_eq2	52.7%	42%	75 bp	33%	16.5
HLFF3BGX5_n02_eq3	50.5%	42%	75 bp	33%	16.2
HLFF3BGX5_n02_eq4	49.6%	41%	75 bp	17%	12.4
HLFF3BGX5_n02_ew0	43.4%	41%	75 bp	25%	11.2
HLFF3BGX5_n02_ew1	43.9%	40%	75 bp	17%	11.5
HLFF3BGX5_n02_ew2	46.0%	41%	75 bp	25%	15.5
HLFF3BGX5_n02_ew3	47.1%	41%	75 bp	25%	14.2
HLFF3BGX5_n02_ew4	51.4%	41%	75 bp	33%	14.8
HLFF3BGX5_n02_hq0	51.8%	41%	75 bp	33%	15.2
HLFF3BGX5_n02_hq1	49.2%	42%	75 bp	25%	16.1
HLFF3BGX5_n02_hq2	52.9%	41%	75 bp	33%	13.8
HLFF3BGX5_n02_hq3	71.0%	45%	75 bp	25%	16.8
HLFF3BGX5_n02_hq4	57.9%	42%	75 bp	25%	13.3
HLFF3BGX5_n02_hw0	56.5%	42%	75 bp	25%	15.2
HLFF3BGX5_n02_hw1	45.1%	42%	75 bp	25%	17.7
HLFF3BGX5_n02_hw2	31.5%	42%	75 bp	25%	17.6
HLFF3BGX5_n02_hw3	45.3%	43%	75 bp	25%	10.9
HLFF3BGX5_n02_hw4	53.7%	42%	75 bp	33%	15.3
HLFF3BGX5_n02_other_stuff_1	49.8%	39%	75 bp	17%	12.5
HLFF3BGX5_n02_other_stuff_2	51.7%	40%	75 bp	25%	17.2
HLFF3BGX5_n02_sq0	69.4%	44%	75 bp	25%	22.5
HLFF3BGX5_n02_sq1	60.1%	42%	75 bp	25%	17.7
HLFF3BGX5_n02_sq2	52.7%	41%	75 bp	25%	11.8
HLFF3BGX5_n02_sq3	56.1%	42%	75 bp	25%	16.1
HLFF3BGX5_n02_sq4	56.6%	41%	75 bp	25%	12.4
HLFF3BGX5_n02_sw0	47.4%	42%	75 bp	25%	10.9
HLFF3BGX5_n02_sw1	38.4%	42%	75 bp	25%	14.2
HLFF3BGX5_n02_sw2	50.3%	42%	75 bp	33%	16.8
HLFF3BGX5_n02_sw3	53.0%	42%	75 bp	33%	17.3
HLFF3BGX5_n02_sw4	54.6%	46%	75 bp	33%	14.7

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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

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	544094620	501744997	4.8	1.1

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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

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 ³²/₃₂ rows and ³/₃ columns.

Library	Total Read Count	Portion (%)	Perfect (%)
eq2	16489010	3.5	97.7
hw4	15308110	3.2	97.6
hw3	10854834	2.3	97.2
eq1	15045599	3.1	97.4
hw2	17627512	3.7	97.4
hq0	15229971	3.2	97.8
ew2	15495393	3.2	97.2
hq2	13829894	2.9	97.5
hq1	16053360	3.4	97.8
eq3	16219556	3.4	97.0
hq4	13283056	2.8	97.6
sw3	17343573	3.6	97.5
sw1	14171769	3.0	97.6
hq3	16794766	3.5	97.5
ew3	14190294	3.0	97.4
sw0	10871573	2.3	97.4
sq2	11845199	2.5	96.5
hw1	17687751	3.7	98.0
sw4	14736788	3.1	97.7
other_stuff_2	17208578	3.6	96.0
sq0	22476152	4.7	97.6
eq0	14356719	3.0	97.5
sq1	17679650	3.7	96.7
sw2	16761572	3.5	97.5
other_stuff_1	12512441	2.6	96.3
ew0	11223735	2.3	97.0
ew4	14827585	3.1	97.3
eq4	12432472	2.6	96.9
sq4	12367911	2.6	97.3
hw0	15222800	3.2	97.5
ew1	11480675	2.4	96.8
sq3	16133254	3.4	96.9

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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 (75bp).

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.

64 samples had less than 1% of reads made up of overrepresented sequences

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

General Statistics: Columns

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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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