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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 1.8

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 2022-09-08, 21:20 based on data in: /gscratch/scrubbed/samwhite/outputs/20220909-pgen-fastqc-fastp-mutliqc-rnaseq

General Statistics

Showing ⁷⁶/₇₆ rows and ⁴/₆ columns.

Sample Name	% Duplication	% > Q30	Mb Q30 bases	GC content	% PF	% Adapter
Geo_Pool_F_GGCTAC_L006_R1_001	70.1%	94.5%	19457.5	43.4%	98.3%	2.8%
Geo_Pool_M_CTTGTA_L006_R1_001	29.2%	92.7%	21409.7	50.7%	97.5%	2.8%
Geoduck-ctenidia-RNA-1_S3_L001_R1_001	26.5%	89.4%	0.8	36.9%	89.5%	1.8%
Geoduck-ctenidia-RNA-2_S11_L002_R1_001	7.9%	86.9%	0.2	37.8%	65.4%	1.5%
Geoduck-ctenidia-RNA-3_S19_L003_R1_001	9.8%	84.5%	0.2	43.0%	70.7%	1.2%
Geoduck-ctenidia-RNA-4_S27_L004_R1_001	5.1%	89.2%	0.8	36.9%	87.1%	1.6%
Geoduck-ctenidia-RNA-5_S35_L005_R1_001	5.7%	93.0%	220.8	36.8%	86.5%	12.7%
Geoduck-ctenidia-RNA-6_S43_L006_R1_001	46.4%	92.6%	14423.0	36.8%	92.6%	6.9%
Geoduck-ctenidia-RNA-7_S51_L007_R1_001	18.3%	90.0%	0.2	38.3%	75.0%	1.7%
Geoduck-ctenidia-RNA-8_S59_L008_R1_001	45.4%	90.6%	1.1	37.3%	90.5%	1.0%
Geoduck-gonad-RNA-1_S1_L001_R1_001	11.5%	79.9%	0.1	43.1%	41.6%	1.3%
Geoduck-gonad-RNA-2_S9_L002_R1_001	2.6%	77.2%	0.2	49.8%	43.0%	1.2%
Geoduck-gonad-RNA-3_S17_L003_R1_001	4.5%	82.3%	0.1	49.5%	20.0%	0.2%
Geoduck-gonad-RNA-4_S25_L004_R1_001	4.2%	79.6%	0.1	57.9%	32.6%	0.5%
Geoduck-gonad-RNA-5_S33_L005_R1_001	5.1%	83.8%	0.0	44.7%	18.3%	0.2%
Geoduck-gonad-RNA-6_S41_L006_R1_001	4.1%	78.4%	0.0	59.2%	14.0%	0.0%
Geoduck-gonad-RNA-7_S49_L007_R1_001	9.0%	77.7%	0.3	39.1%	57.6%	1.2%
Geoduck-gonad-RNA-8_S57_L008_R1_001	77.4%	92.4%	13256.1	37.6%	89.8%	8.4%
Geoduck-heart-RNA-1_S2_L001_R1_001	56.5%	88.3%	1.6	38.4%	92.8%	2.0%
Geoduck-heart-RNA-2_S10_L002_R1_001	5.9%	85.4%	0.7	38.2%	70.8%	1.1%
Geoduck-heart-RNA-3_S18_L003_R1_001	34.2%	92.6%	3.7	36.8%	93.7%	1.9%
Geoduck-heart-RNA-4_S26_L004_R1_001	2.6%	87.2%	1.7	38.5%	88.1%	1.4%
Geoduck-heart-RNA-5_S34_L005_R1_001	3.4%	85.2%	23.8	39.0%	96.0%	1.5%
Geoduck-heart-RNA-6_S42_L006_R1_001	24.6%	89.7%	0.4	39.5%	76.7%	1.2%
Geoduck-heart-RNA-7_S50_L007_R1_001	23.7%	90.1%	26328.7	38.6%	98.1%	1.7%
Geoduck-heart-RNA-8_S58_L008_R1_001	27.3%	90.1%	4.8	38.4%	95.1%	2.3%
Geoduck-juvenile-OA-exposure-RNA-EPI-115-1_S4_L001_R1_001	12.1%	85.5%	0.5	44.8%	69.2%	1.6%
Geoduck-juvenile-OA-exposure-RNA-EPI-115-2_S12_L002_R1_001	1.5%	81.4%	0.1	44.9%	19.8%	0.4%
Geoduck-juvenile-OA-exposure-RNA-EPI-115-3_S20_L003_R1_001	3.4%	77.5%	0.5	46.4%	54.0%	1.3%
Geoduck-juvenile-OA-exposure-RNA-EPI-115-4_S28_L004_R1_001	9.3%	92.0%	354.4	38.7%	96.4%	3.7%
Geoduck-juvenile-OA-exposure-RNA-EPI-115-5_S36_L005_R1_001	61.6%	92.6%	20307.9	38.8%	96.7%	3.6%
Geoduck-juvenile-OA-exposure-RNA-EPI-115-6_S44_L006_R1_001	22.2%	90.1%	0.3	40.5%	55.6%	0.6%
Geoduck-juvenile-OA-exposure-RNA-EPI-115-7_S52_L007_R1_001	2.1%	75.8%	13.0	38.7%	81.1%	2.6%
Geoduck-juvenile-OA-exposure-RNA-EPI-115-8_S60_L008_R1_001	44.1%	90.7%	0.5	39.5%	65.9%	1.6%
Geoduck-juvenile-OA-exposure-RNA-EPI-116-1_S5_L001_R1_001	51.1%	90.3%	0.8	38.3%	87.6%	1.4%
Geoduck-juvenile-OA-exposure-RNA-EPI-116-2_S13_L002_R1_001	9.3%	88.8%	0.1	38.6%	36.9%	1.1%
Geoduck-juvenile-OA-exposure-RNA-EPI-116-3_S21_L003_R1_001	4.6%	91.7%	156.9	38.0%	95.8%	4.3%
Geoduck-juvenile-OA-exposure-RNA-EPI-116-4_S29_L004_R1_001	16.2%	91.4%	23455.3	38.0%	98.1%	2.3%
Geoduck-juvenile-OA-exposure-RNA-EPI-116-5_S37_L005_R1_001	45.0%	91.4%	0.9	37.7%	88.3%	1.4%
Geoduck-juvenile-OA-exposure-RNA-EPI-116-6_S45_L006_R1_001	26.9%	88.1%	0.2	41.7%	50.5%	1.3%
Geoduck-juvenile-OA-exposure-RNA-EPI-116-7_S53_L007_R1_001	10.4%	90.5%	0.2	38.7%	52.9%	0.6%
Geoduck-juvenile-OA-exposure-RNA-EPI-116-8_S61_L008_R1_001	80.7%	91.0%	5.1	37.4%	96.9%	1.5%
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-1_S6_L001_R1_001	2.8%	78.3%	0.1	55.8%	58.6%	1.8%
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-2_S14_L002_R1_001	7.4%	91.1%	520.6	36.4%	97.1%	2.4%
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-3_S22_L003_R1_001	32.5%	92.7%	15708.5	36.7%	97.6%	2.5%
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-4_S30_L004_R1_001	13.8%	91.4%	0.2	38.2%	73.9%	0.4%
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-5_S38_L005_R1_001	12.3%	79.3%	0.2	39.8%	56.1%	1.4%
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-6_S46_L006_R1_001	5.8%	86.5%	0.2	39.4%	69.7%	1.3%
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-7_S54_L007_R1_001	23.5%	90.5%	15.7	38.6%	97.4%	1.7%
Geoduck-juvenile-ambient-exposure-RNA-EPI-123-8_S62_L008_R1_001	41.2%	90.2%	0.1	42.3%	59.5%	1.4%
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-1_S7_L001_R1_001	41.6%	83.4%	2.0	37.8%	89.9%	1.9%
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-2_S15_L002_R1_001	18.9%	87.0%	22723.4	36.9%	96.8%	1.6%
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-3_S23_L003_R1_001	4.3%	77.2%	0.4	39.5%	65.1%	1.9%
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-4_S31_L004_R1_001	2.1%	83.1%	0.1	48.1%	34.5%	0.2%
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-5_S39_L005_R1_001	39.5%	83.4%	0.2	37.4%	63.7%	0.2%
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-6_S47_L006_R1_001	26.8%	80.6%	0.1	46.3%	57.0%	0.8%
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-7_S55_L007_R1_001	3.1%	85.2%	0.3	39.0%	72.6%	2.4%
Geoduck-juvenile-ambient-exposure-RNA-EPI-124-8_S63_L008_R1_001	9.0%	82.1%	4.3	38.6%	89.4%	4.6%
Geoduck-larvae-day5-RNA-EPI-99-1_S8_L001_R1_001	54.2%	91.7%	15623.4	38.7%	96.6%	3.2%
Geoduck-larvae-day5-RNA-EPI-99-2_S16_L002_R1_001	6.4%	82.0%	0.1	51.7%	39.0%	0.4%
Geoduck-larvae-day5-RNA-EPI-99-3_S24_L003_R1_001	1.0%	73.5%	0.3	62.1%	52.9%	1.2%
Geoduck-larvae-day5-RNA-EPI-99-4_S32_L004_R1_001	6.0%	89.2%	0.2	43.1%	65.8%	1.1%
Geoduck-larvae-day5-RNA-EPI-99-5_S40_L005_R1_001	64.4%	92.5%	11.1	38.9%	95.4%	2.4%
Geoduck-larvae-day5-RNA-EPI-99-6_S48_L006_R1_001	0.0%	69.5%	0.0	74.6%	20.5%	0.4%
Geoduck-larvae-day5-RNA-EPI-99-7_S56_L007_R1_001	0.0%	79.5%	0.1	50.1%	29.7%	1.3%
Geoduck-larvae-day5-RNA-EPI-99-8_S64_L008_R1_001	25.6%	84.4%	0.1	45.2%	55.1%	0.8%
Trueseq-stranded-mRNA-libraries-GeoRNA1-A1-NR006_S1_L001_R1_001	38.7%	94.0%	915.1	37.2%	91.2%	4.1%
Trueseq-stranded-mRNA-libraries-GeoRNA1-A1-NR006_S1_L002_R1_001	39.1%	93.9%	923.2	37.1%	91.2%	4.0%
Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L001_R1_001	4.3%	91.9%	19.5	36.0%	92.3%	1.4%
Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L002_R1_001	4.6%	91.8%	19.3	36.0%	92.4%	1.4%
Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L001_R1_001	3.9%	92.5%	13.0	37.8%	95.9%	1.9%
Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L002_R1_001	4.1%	92.4%	13.0	37.8%	95.5%	2.0%
Trueseq-stranded-mRNA-libraries-GeoRNA7-G1-NR019_S4_L001_R1_001	0.1%	60.1%	26.6	27.1%	65.1%	0.8%
Trueseq-stranded-mRNA-libraries-GeoRNA7-G1-NR019_S4_L002_R1_001	0.1%	59.7%	25.9	27.1%	64.2%	0.8%
Trueseq-stranded-mRNA-libraries-GeoRNA8-H1-NR021_S5_L001_R1_001	0.0%	0.0%	0.0	0.0%	0.0%	0.0%
Trueseq-stranded-mRNA-libraries-GeoRNA8-H1-NR021_S5_L002_R1_001	12.7%	93.4%	1041.1	38.5%	97.2%	1.8%

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Sort	Group	Column	Description	ID	Scale
\|\|	fastp	% Duplication	Duplication rate in filtered reads	`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

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.

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General Statistics

General Statistics: Columns

fastp

Filtered Reads

Duplication Rates

Insert Sizes

Sequence Quality

GC Content

N content

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