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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 1.24.1

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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:

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

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Report generated on 2025-07-16, 00:22 PDT based on data in: /mmfs1/gscratch/scrubbed/samwhite/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/02.20-D-Apul-RNAseq-alignment-HiSat2

General Statistics

Showing ⁸⁰/₈₀ rows and ²/₄ columns.

Sample Name	Reads	Reads mapped	% Reads mapped	% Aligned
ACR-139-TP1-hisat2_output	40.5M	31.6M	78.1%
ACR-139-TP1_hisat2				75.0%
ACR-139-TP2-hisat2_output	42.9M	32.4M	75.4%
ACR-139-TP2_hisat2				72.7%
ACR-139-TP3-hisat2_output	40.7M	32.9M	80.7%
ACR-139-TP3_hisat2				78.2%
ACR-139-TP4-hisat2_output	46.4M	36.5M	78.5%
ACR-139-TP4_hisat2				75.4%
ACR-145-TP1-hisat2_output	55.9M	45.2M	80.8%
ACR-145-TP1_hisat2				75.2%
ACR-145-TP2-hisat2_output	39.2M	25.3M	64.5%
ACR-145-TP2_hisat2				60.7%
ACR-145-TP3-hisat2_output	51.8M	39.7M	76.7%
ACR-145-TP3_hisat2				73.8%
ACR-145-TP4-hisat2_output	48.8M	36.2M	74.3%
ACR-145-TP4_hisat2				70.7%
ACR-150-TP1-hisat2_output	54.2M	38.9M	71.8%
ACR-150-TP1_hisat2				66.7%
ACR-150-TP2-hisat2_output	42.4M	34.2M	80.6%
ACR-150-TP2_hisat2				77.6%
ACR-150-TP3-hisat2_output	40.5M	32.6M	80.6%
ACR-150-TP3_hisat2				77.7%
ACR-150-TP4-hisat2_output	46.6M	37.9M	81.3%
ACR-150-TP4_hisat2				79.3%
ACR-173-TP1-hisat2_output	47.0M	36.7M	78.1%
ACR-173-TP1_hisat2				71.8%
ACR-173-TP2-hisat2_output	37.0M	27.8M	75.2%
ACR-173-TP2_hisat2				71.3%
ACR-173-TP3-hisat2_output	46.5M	36.7M	78.9%
ACR-173-TP3_hisat2				76.4%
ACR-173-TP4-hisat2_output	39.8M	30.1M	75.7%
ACR-173-TP4_hisat2				71.9%
ACR-186-TP1-hisat2_output	36.1M	22.1M	61.2%
ACR-186-TP1_hisat2				57.7%
ACR-186-TP2-hisat2_output	39.0M	30.4M	78.0%
ACR-186-TP2_hisat2				75.0%
ACR-186-TP3-hisat2_output	35.6M	27.3M	76.7%
ACR-186-TP3_hisat2				74.5%
ACR-186-TP4-hisat2_output	41.9M	34.2M	81.6%
ACR-186-TP4_hisat2				79.0%
ACR-225-TP1-hisat2_output	38.6M	30.6M	79.5%
ACR-225-TP1_hisat2				76.1%
ACR-225-TP2-hisat2_output	44.7M	34.8M	78.0%
ACR-225-TP2_hisat2				74.7%
ACR-225-TP3-hisat2_output	47.0M	37.2M	79.2%
ACR-225-TP3_hisat2				76.1%
ACR-225-TP4-hisat2_output	36.4M	28.0M	76.9%
ACR-225-TP4_hisat2				73.6%
ACR-229-TP1-hisat2_output	49.6M	41.0M	82.7%
ACR-229-TP1_hisat2				80.1%
ACR-229-TP2-hisat2_output	41.8M	33.3M	79.7%
ACR-229-TP2_hisat2				77.5%
ACR-229-TP3-hisat2_output	38.7M	31.2M	80.7%
ACR-229-TP3_hisat2				78.2%
ACR-229-TP4-hisat2_output	52.0M	38.0M	73.1%
ACR-229-TP4_hisat2				69.0%
ACR-237-TP1-hisat2_output	49.3M	39.1M	79.3%
ACR-237-TP1_hisat2				76.9%
ACR-237-TP2-hisat2_output	37.0M	26.9M	72.6%
ACR-237-TP2_hisat2				69.6%
ACR-237-TP3-hisat2_output	39.5M	32.4M	82.1%
ACR-237-TP3_hisat2				79.9%
ACR-237-TP4-hisat2_output	54.8M	43.4M	79.2%
ACR-237-TP4_hisat2				76.0%
ACR-244-TP1-hisat2_output	41.4M	21.3M	51.4%
ACR-244-TP1_hisat2				48.4%
ACR-244-TP2-hisat2_output	48.1M	36.0M	74.9%
ACR-244-TP2_hisat2				72.2%
ACR-244-TP3-hisat2_output	51.8M	41.4M	79.8%
ACR-244-TP3_hisat2				76.5%
ACR-244-TP4-hisat2_output	49.2M	36.7M	74.6%
ACR-244-TP4_hisat2				71.5%
ACR-265-TP1-hisat2_output	69.8M	53.6M	76.8%
ACR-265-TP1_hisat2				72.3%
ACR-265-TP2-hisat2_output	47.9M	38.0M	79.3%
ACR-265-TP2_hisat2				76.7%
ACR-265-TP3-hisat2_output	50.6M	39.7M	78.5%
ACR-265-TP3_hisat2				74.4%
ACR-265-TP4-hisat2_output	53.8M	40.8M	75.8%
ACR-265-TP4_hisat2				72.8%

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

Sort	Group	Column	Description	ID	Scale
\|\|	Samtools: flagstat	Reads	Total reads in the bam file (millions)	`flagstat_total`	read_count
\|\|	Samtools: flagstat	Reads mapped	Reads mapped in the bam file (millions)	`mapped_passed`	read_count
\|\|	Samtools: flagstat	% Reads mapped	% Reads mapped in the bam file	`mapped_passed_pct`
\|\|	Bowtie 2 / HiSAT2	% Aligned	overall alignment rate	`overall_alignment_rate`

Samtools

Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

Flagstat

This module parses the output from samtools flagstat

Created with MultiQC

Showing ⁴⁰/₄₀ rows and ¹¹/₁₁ columns.

Sample Name	Total Reads	Total Passed QC	Mapped	Secondary Alignments	Paired in Sequencing	Properly Paired	Self and mate mapped	Singletons	Mate mapped to diff chr	Diff chr (mapQ >= 5)
ACR-139-TP1-hisat2_output	40514601	40514601	31644044	5088507	35426094	21811588	24359840	2195697	186360	103532
ACR-139-TP2-hisat2_output	42904338	42904338	32362061	4335510	38568828	23263232	25848236	2178315	147814	83548
ACR-139-TP3-hisat2_output	40692395	40692395	32856425	4775143	35917252	22437088	26037950	2043332	125070	64994
ACR-139-TP4-hisat2_output	46419221	46419221	36451171	5935009	40484212	24470950	28215652	2300510	189820	98888
ACR-145-TP1-hisat2_output	55888296	55888296	45161238	12722498	43165798	25445716	30315876	2122864	198208	91367
ACR-145-TP2-hisat2_output	39220770	39220770	25300311	3832016	35388754	17477094	20004756	1463539	106568	55165
ACR-145-TP3-hisat2_output	51798755	51798755	39742302	5706631	46092124	24893998	31771330	2264341	172336	77211
ACR-145-TP4-hisat2_output	48763252	48763252	36226167	6009128	42754124	23358292	27963846	2253193	187328	93285
ACR-150-TP1-hisat2_output	54180266	54180266	38904880	8284816	45895450	22545856	28788764	1831300	200580	75068
ACR-150-TP2-hisat2_output	42383163	42383163	34169086	5768531	36614632	23210154	26478818	1921737	149774	79882
ACR-150-TP3-hisat2_output	40498238	40498238	32629364	5252792	35245446	22518420	25350788	2025784	173678	93328
ACR-150-TP4-hisat2_output	46596213	46596213	37880626	4389957	42206256	27599718	31123486	2367183	169724	93486
ACR-173-TP1-hisat2_output	46990215	46990215	36680081	10382259	36607956	19950804	24326896	1970926	251380	111943
ACR-173-TP2-hisat2_output	36982058	36982058	27797302	4920634	32061424	18645248	21109948	1766720	143370	78212
ACR-173-TP3-hisat2_output	46524236	46524236	36720695	5006112	41518124	24519378	29484278	2230305	148828	72660
ACR-173-TP4-hisat2_output	39792121	39792121	30116176	5345161	34446960	18429490	23255134	1515881	141408	54970
ACR-186-TP1-hisat2_output	36091405	36091405	22090136	3005123	33086282	13628386	18025560	1059453	107004	38680
ACR-186-TP2-hisat2_output	38990573	38990573	30392414	4628915	34361658	21297136	23865138	1898361	121742	68142
ACR-186-TP3-hisat2_output	35551004	35551004	27270193	3063070	32487934	18462044	22479526	1727597	110094	53318
ACR-186-TP4-hisat2_output	41898404	41898404	34192248	5148604	36749800	23846658	26977464	2066180	138046	77810
ACR-225-TP1-hisat2_output	38552065	38552065	30632941	5464575	33087490	19983320	23389850	1778516	120890	61308
ACR-225-TP2-hisat2_output	44658755	44658755	34843641	5803253	38855502	23316812	26523300	2517088	220836	119694
ACR-225-TP3-hisat2_output	46972696	46972696	37224412	6149224	40823472	24633262	28747414	2327774	172540	87509
ACR-225-TP4-hisat2_output	36448522	36448522	28032380	4580038	31868484	18170842	21884438	1567904	110262	52007
ACR-229-TP1-hisat2_output	49612813	49612813	41042399	6505735	43107078	27952968	32056694	2479970	183648	100577
ACR-229-TP2-hisat2_output	41803881	41803881	33313398	4129395	37674486	23475538	26897182	2286821	170126	92566
ACR-229-TP3-hisat2_output	38655660	38655660	31201869	4484470	34171190	21790608	24560170	2157229	165360	91208
ACR-229-TP4-hisat2_output	52002278	52002278	38018518	6953202	45049076	22135784	29152648	1912668	176306	72834
ACR-237-TP1-hisat2_output	49277546	49277546	39059350	5060792	44216754	25970038	31853474	2145084	170036	80198
ACR-237-TP2-hisat2_output	37016338	37016338	26888120	3729080	33287258	18747178	21396432	1762608	136010	73373
ACR-237-TP3-hisat2_output	39521107	39521107	32434483	4195639	35325468	23465304	26268816	1970028	155094	85564
ACR-237-TP4-hisat2_output	54813649	54813649	43422970	7327451	47486198	28149436	33886736	2208783	155842	77029
ACR-244-TP1-hisat2_output	41350464	41350464	21271892	2451050	38899414	14997776	17527392	1293450	89194	45353
ACR-244-TP2-hisat2_output	48088052	48088052	36034495	4708162	43379890	25398860	28962220	2364113	204132	108790
ACR-244-TP3-hisat2_output	51809330	51809330	41354431	7248262	44561068	27836940	31254796	2851373	278450	153140
ACR-244-TP4-hisat2_output	49202140	49202140	36699713	5294522	43907618	23269916	29462984	1942207	142016	63095
ACR-265-TP1-hisat2_output	69842228	69842228	53602337	11241758	58600470	31296266	39770434	2590145	231424	97985
ACR-265-TP2-hisat2_output	47914940	47914940	37997824	5278662	42636278	26083342	30155814	2563348	212428	114076
ACR-265-TP3-hisat2_output	50566296	50566296	39720352	8191892	42374404	24244612	29150952	2377508	234396	112862
ACR-265-TP4-hisat2_output	53756971	53756971	40764652	6027143	47729828	26498028	32586594	2150915	145264	66811

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: table-samtools-flagstat-dp

Sort	Column	Description	ID	Scale
\|\|	Total Reads	Total Reads	`flagstat_total`	read_count
\|\|	Total Passed QC	Total Passed QC	`total_passed`	read_count
\|\|	Mapped	Mapped	`mapped_passed`	read_count
\|\|	Secondary Alignments	Secondary Alignments	`secondary_passed`	read_count
\|\|	Duplicates	Duplicates	`duplicates_passed`	read_count
\|\|	Paired in Sequencing	Paired in Sequencing	`paired in sequencing_passed`	read_count
\|\|	Properly Paired	Properly Paired	`properly paired_passed`	read_count
\|\|	Self and mate mapped	Reads with itself and mate mapped	`with itself and mate mapped_passed`	read_count
\|\|	Singletons	Singletons	`singletons_passed`	read_count
\|\|	Mate mapped to diff chr	Mate mapped to different chromosome	`with mate mapped to a different chr_passed`	read_count
\|\|	Diff chr (mapQ >= 5)	Mate mapped to different chromosome (mapQ >= 5)	`with mate mapped to a different chr (mapQ >= 5)_passed`	read_count

Bowtie 2 / HiSAT2

Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4

Paired-end alignments

This plot shows the number of reads aligning to the reference in different ways.

Please note that single mate alignment counts are halved to tally with pair counts properly.

There are 6 possible types of alignment:

PE mapped uniquely: Pair has only one occurence in the reference genome.
PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
PE one mate mapped uniquely: One read of a pair has one occurence.
PE multimapped: Pair has multiple occurence.
PE one mate multimapped: One read of a pair has multiple occurence.
PE neither mate aligned: Pair has no occurence.

Created with MultiQC

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Samtools: flagstat: read count: Columns

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Paired-end alignments Help

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Paired-end alignments