MultiQC Report

v1.10.1 (eef03df)

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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 1.10.1 (eef03df)

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

Samtools

Sample Name	M Reads	M Reads Mapped	N50 (Kbp)	Length (Mbp)	% Duplication	% > Q30	Mb Q30 bases	GC content	% PF	% Adapter
CV18	2.9	0.0	29.9Kbp	0.0Mbp	38.5%	97.3%	320.4	50.2%	99.7%	2.2%
CV29	1.5	0.0	30.0Kbp	0.0Mbp	30.9%	96.9%	175.4	45.7%	99.3%	0.3%

Sort	Group	Column	Description	ID	Scale
\|\|	Samtools	M Reads	Total reads in the bam file (millions)	`flagstat_total`	read_count
\|\|	Samtools	M Reads Mapped	Reads Mapped in the bam file (millions)	`mapped_passed`	read_count
\|\|	QUAST	N50 (Kbp)	N50 is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly (kilo base pairs)	`N50`	None
\|\|	QUAST	Length (Mbp)	The total number of bases in the assembly (mega base pairs).	`Total length`	None
\|\|	fastp	% Duplication	Duplication rate before filtering	`pct_duplication`	None
\|\|	fastp	% > Q30	Percentage of reads > Q30 after filtering	`after_filtering_q30_rate`	None
\|\|	fastp	Mb Q30 bases	Bases > Q30 after filtering (millions)	`after_filtering_q30_bases`	base_count
\|\|	fastp	GC content	GC content after filtering	`after_filtering_gc_content`	None
\|\|	fastp	% PF	Percent reads passing filter	`pct_surviving`	None
\|\|	fastp	% Adapter	Percentage adapter-trimmed reads	`pct_adapter`	None

Sample Name	N50 (Kbp)	N75 (Kbp)	L50 (K)	L75 (K)	Largest contig (Kbp)	Length (Mbp)	Misassemblies	Mismatches/100kbp	Indels/100kbp	Genome Fraction
CV18	29.9Kbp	29.9Kbp	0.0K	1.0K	29.9Kbp	0.0Mbp	0.0	33.52	0.00	99.8%
CV29	30.0Kbp	30.0Kbp	0.0K	1.0K	30.0Kbp	0.0Mbp	0.0	23.59	0.00	99.2%

Sort	Group	Column	Description	ID	Scale
\|\|	QUAST	N50 (Kbp)	N50 is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly.	`N50`	None
\|\|	QUAST	N75 (Kbp)	N75 is the contig length such that using longer or equal length contigs produces 75% of the bases of the assembly	`N75`	None
\|\|	QUAST	L50 (K)	L50 is the number of contigs larger than N50, i.e. the minimum number of contigs comprising 50% of the total assembly length.	`L50`	None
\|\|	QUAST	L75 (K)	L75 is the number of contigs larger than N75, i.e. the minimum number of contigs comprising 75% of the total assembly length.	`L75`	None
\|\|	QUAST	Largest contig (Kbp)	The size of the largest contig of the assembly	`Largest contig`	None
\|\|	QUAST	Length (Mbp)	The total number of bases in the assembly.	`Total length`	None
\|\|	QUAST	Misassemblies	The number of positions in the assembled contigs where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference (relocation) or they overlap on more than 1 kbp (relocation) or flanking sequences align on different strands (inversion) or different chromosomes (translocation).	`# misassemblies`	None
\|\|	QUAST	Mismatches/100kbp	The number of mismatches per 100 kbp	`# mismatches per 100 kbp`	None
\|\|	QUAST	Indels/100kbp	The number of indels per 100 kbp	`# indels per 100 kbp`	None
\|\|	QUAST	Genome Fraction	The total number of aligned bases in the reference, divided by the genome size.	`Genome fraction (%)`	None

Samtools is a suite of programs for interacting with high-throughput sequencing data.

Samtools Flagstat

This module parses the output from samtools flagstat. All numbers in millions.

fastp

fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)

Filtered Reads

Filtering statistics of sampled reads.

Duplication Rates

Duplication rates of sampled reads.

Insert Sizes

Insert size estimation of sampled reads.

Sequence Quality

Average sequencing quality over each base of all reads.

GC Content

Average GC content over each base of all reads.

N content

Average N content over each base of all reads.

v1.10.1 (eef03df)

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General Statistics

QUAST

Assembly Statistics

Number of Contigs

Samtools

Samtools Flagstat

fastp

Filtered Reads

Duplication Rates

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Sequence Quality

GC Content

N content

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General Statistics: Columns

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Assembly Statistics

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Number of Contigs

Samtools

Samtools Flagstat

fastp

Filtered Reads

Duplication Rates

Insert Sizes

Sequence Quality

GC Content

N content

v1.10.1 (eef03df)

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