MultiQC Report

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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

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

QualiMap

Sample Name	Avg. GC	Insert Size	≥ 1X	≥ 5X	≥ 10X	≥ 30X	≥ 50X	Coverage	% Aligned	M Aligned	M Total reads	Median Coverage	Bases ≥ 30X
A36971_1_lane									99.6%	893.7	897.3	35.0X	67%
A36971_1_lane_stats	41%	427bp	91.6%	91.5%	91.4%	67.5%	16.4%	36.0X
A79947_1_lane									98.9%	1028.3	1039.6	31.0X	54%
A79947_1_lane_stats	41%	363bp	91.6%	91.5%	91.3%	59.2%	9.2%	33.0X
COLO829_2_lanes_dupsFlagged									97.9%	1003.3	1024.7	24.0X	33%
COLO829_2_lanes_dupsFlagged_stats	43%	176bp	91.5%	91.1%	90.0%	63.5%	23.4%	36.0X
GSC2_2_lanes_dupsFlagged									97.0%	630.4	650.2	16.0X	5%
GSC2_2_lanes_dupsFlagged_stats	43%	169bp	91.4%	90.2%	85.2%	28.8%	2.7%	23.0X
HL60_GSC.spec									99.7%	927.3	930.4	38.0X	79%
HL60_GSC.spec_stats	42%	374bp	91.6%	91.5%	91.4%	77.2%	15.3%	39.0X

Sort	Group	Column	Description	ID	Scale
\|\|	QualiMap	Avg. GC	Average GC content	`avg_gc`	None
\|\|	QualiMap	Insert Size	Median insert size	`median_insert_size`	None
\|\|	QualiMap	≥ 1X	Fraction of genome with at least 1X coverage	`1_x_pc`	None
\|\|	QualiMap	≥ 5X	Fraction of genome with at least 5X coverage	`5_x_pc`	None
\|\|	QualiMap	≥ 10X	Fraction of genome with at least 10X coverage	`10_x_pc`	None
\|\|	QualiMap	≥ 30X	Fraction of genome with at least 30X coverage	`30_x_pc`	None
\|\|	QualiMap	≥ 50X	Fraction of genome with at least 50X coverage	`50_x_pc`	None
\|\|	QualiMap	Coverage	Median coverage	`median_coverage`	None
\|\|	QualiMap	% Aligned	% mapped reads	`percentage_aligned`	None
\|\|	QualiMap	M Aligned	Number of mapped reads (millions)	`mapped_reads`	read_count
\|\|	QualiMap	M Total reads	Number of reads (millions)	`total_reads`	read_count
\|\|	Picard	Median Coverage	The median coverage in bases of the genome territory, after all filters are applied.	`MEDIAN_COVERAGE`	None
\|\|	Picard	Bases ≥ 30X	Percent of target bases with coverage ≥ 30X	`PCT_30X`	None

QualiMap is a platform-independent application to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

Coverage histogram

Cumulative coverage genome fraction

Insert size histogram

GC content distribution

Picard

Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

GC Coverage Bias

This plot shows bias in coverage across regions of the genome with varying GC content. A perfect library would be a flat line at y = 1.

WGS Coverage

The number of bases in the genome territory for each fold coverage. Note that final 1% of data is hidden to prevent very long tails.

WGS Filtered Bases

For more information about the filtered categories, see the Picard documentation.

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General Statistics

General Statistics: Columns

QualiMap

Coverage histogram

Cumulative coverage genome fraction

Insert size histogram

GC content distribution

Picard

GC Coverage Bias

WGS Coverage

WGS Filtered Bases

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