MultiQC Report

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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 1.33

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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

MultiQC is developed by Seqera.

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

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Report generated on 2026-02-25, 15:30 AST based on data in:

/home/abbey/medi/data/preprocessed
/home/abbey/medi/data/kraken2

General Statistics

Showing ⁴²/₄₂ rows and ⁵/₈ columns.

Sample Name	% Duplication	% > Q30	Mb Q30 bases	Reads After Filtering	GC content	% PF	% Adapter	Mean R1 Length
EDM001W0_merged.hifi_reads	0.0%	99.7%	438.7Mb	0.2M	43.7%	98.7%	0.4%	2586.0bp
EDM001W6_merged.hifi_reads	0.0%	99.6%	120.8Mb	0.0M	49.2%	98.6%	0.4%	2850.0bp
EDM002W0_merged.hifi_reads	0.0%	99.6%	484.4Mb	0.1M	43.8%	98.7%	0.5%	3732.0bp
EDM002W6_merged.hifi_reads	0.0%	99.7%	107.9Mb	0.0M	44.5%	98.5%		3250.0bp
EDM005W0_merged.hifi_reads	0.2%	99.5%	467.9Mb	0.1M	46.7%	98.2%	0.5%	4431.0bp
EDM005W6_merged.hifi_reads	0.0%	99.5%	266.4Mb	0.1M	44.4%	98.5%		3483.0bp
EDM005W12_merged.hifi_reads	0.0%	99.5%	48.8Mb	0.0M	48.3%	98.5%		4024.0bp
HAI008W0_merged.hifi_reads	0.0%	99.6%	139.6Mb	0.1M	43.0%	98.3%	0.7%	2813.0bp
HAI008W6_merged.hifi_reads	0.1%	99.6%	849.0Mb	0.3M	43.1%	98.7%	0.9%	3236.0bp
HAI008W12_merged.hifi_reads	0.1%	99.5%	1182.0Mb	0.4M	42.2%	98.6%	0.8%	3477.0bp
HFX006W0_merged.hifi_reads	0.0%	99.6%	136.2Mb	0.0M	41.3%	98.7%		3502.0bp
HFX006W6_merged.hifi_reads	0.0%	99.6%	233.0Mb	0.1M	42.3%	98.7%		3073.0bp
HFX009W0.hifi_reads	0.5%	99.5%	16637.2Mb	3.6M	44.5%	98.4%		4966.0bp
HFX009W6.hifi_reads	0.0%	99.5%	1117.3Mb	0.3M	45.0%	98.1%		4228.0bp
HFX011W0.hifi_reads	0.0%	99.5%	1018.6Mb	0.3M	46.6%	98.4%		3470.0bp
HFX011W6.hifi_reads	0.0%	99.5%	80.7Mb	0.0M	46.6%	98.7%	1.0%	2584.0bp
HFX011W12_merged.hifi_reads	0.1%	99.6%	3932.2Mb	1.2M	42.2%	98.8%		3419.0bp
JER002W0.hifi_reads	1.0%	99.3%	8542.3Mb	1.6M	45.7%	96.9%		6298.0bp
JER002W6.hifi_reads	0.0%	99.5%	111.4Mb	0.0M	44.6%	97.9%		3992.0bp
JER003W0_merged.hifi_reads	1.4%	99.6%	5228.3Mb	1.3M	44.0%	98.6%		4189.0bp
JER003W6_merged.hifi_reads	0.1%	99.6%	2288.8Mb	0.7M	44.9%	98.7%		3510.0bp
JER003W12_merged.hifi_reads	0.0%	99.7%	864.5Mb	0.3M	44.7%	98.8%		2955.0bp
JER004W0_merged.hifi_reads	0.0%	99.6%	1003.7Mb	0.3M	44.1%	98.6%		3106.0bp
JER004W6_merged.hifi_reads	0.0%	99.6%	202.2Mb	0.1M	44.5%	98.7%		3164.0bp
JER007W0.hifi_reads	0.0%	99.3%	10360.8Mb	1.9M	41.5%	98.1%		6050.0bp
JER007W6_merged.hifi_reads	0.0%	99.5%	27.5Mb	0.0M	50.6%	98.2%	9.0%	3116.0bp
JER014W0_merged.hifi_reads	0.2%	99.6%	2195.7Mb	0.7M	42.6%	98.8%	1.5%	3374.0bp
TLV004W0.hifi_reads	0.1%	99.5%	1527.0Mb	0.4M	44.2%	98.1%		4358.0bp
TLV004W6_merged.hifi_reads	0.0%	99.5%	363.8Mb	0.1M	56.8%	98.3%	2.4%	2626.0bp
TLV008W0_merged.hifi_reads	0.0%	99.6%	147.9Mb	0.1M	46.0%	98.7%		2798.0bp
TLV008W6_merged.hifi_reads	0.0%	99.6%	97.0Mb	0.0M	48.3%	98.9%	1.4%	2969.0bp
TLV011W0_merged.hifi_reads	0.0%	99.6%	510.6Mb	0.2M	44.6%	98.7%	0.8%	2796.0bp
TLV011W6_merged.hifi_reads	0.1%	99.7%	38.7Mb	0.0M	42.0%	98.9%	0.6%	2904.0bp
TLV011W12_merged.hifi_reads	0.0%	99.7%	53.8Mb	0.0M	41.1%	99.0%		3498.0bp
TLV019W0.hifi_reads	0.1%	99.4%	11510.2Mb	2.5M	50.0%	98.2%		4970.0bp
TLV019W6_merged.hifi_reads	0.0%	99.5%	1368.1Mb	0.4M	47.4%	97.9%	0.9%	3922.0bp
TLV021W0.hifi_reads	0.0%	99.5%	2.3Mb	0.0M	43.9%	99.3%		3649.0bp
TLV021W6_merged.hifi_reads	0.0%	99.6%	272.3Mb	0.1M	46.0%	98.8%	1.1%	3325.0bp
TLV021W12_merged.hifi_reads	0.0%	99.5%	153.0Mb	0.0M	47.9%	98.7%		4153.0bp
TLV023W0_merged.hifi_reads	0.9%	99.6%	3044.7Mb	0.8M	43.0%	98.7%		4058.0bp
TLV023W6_merged.hifi_reads	0.9%	99.6%	2194.8Mb	0.6M	43.1%	98.8%	0.9%	3699.0bp
TLV023W12_merged.hifi_reads	0.5%	99.6%	209.2Mb	0.1M	43.4%	97.8%	1.5%	3465.0bp

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: general_stats_table_table

Sort	Group	Column	Description	ID	Scale
\|\|	fastp	% Duplication	Duplication rate before filtering	`fastp-pct_duplication`
\|\|	fastp	% > Q30	Percentage of reads > Q30 after filtering	`fastp-after_filtering_q30_rate`
\|\|	fastp	Mb Q30 bases	Bases > Q30 after filtering (millions)	`fastp-after_filtering_q30_bases`	base_count
\|\|	fastp	Reads After Filtering	Total reads after filtering (millions)	`fastp-filtering_result_passed_filter_reads`	read_count
\|\|	fastp	GC content	GC content after filtering	`fastp-after_filtering_gc_content`
\|\|	fastp	% PF	Percent reads passing filter	`fastp-pct_surviving`
\|\|	fastp	% Adapter	Percentage adapter-trimmed reads	`fastp-pct_adapter`
\|\|	fastp	Mean R1 Length	Mean read length of R1	`fastp-before_filtering_read1_mean_length`

fastp

Version:


                      
                        1.0.1

All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

Filtered Reads

Filtering statistics of sampled reads.

Created with MultiQC

Sequence Quality

Average sequencing quality over each base of all reads.

Created with MultiQC

GC Content

Average GC content over each base of all reads.

Created with MultiQC

N content

Average N content over each base of all reads.

Created with MultiQC

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Software	Version
fastp	`1.0.1`

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