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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 1.12

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

BJ-WGS v1.6.0

The report aggregates all metrics from WGS analyses to help evaluate the performance of single-cell libraries.

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Report generated on 2022-10-27, 05:37 based on data in: /tmp/nxf.hr8t7eMAbs

General Statistics

Showing ⁴/₄ rows and ⁴/₆ columns.

Sample Name	Change rate	Ts/Tv	M Variants	% Aligned	Insert Size	Mean Insert Size
MultiSample	109179	2.632	0.03
NA12878v2-SC1	132905	2.592	0.02	100%	299 bp	325 bp
NA12878v2-SC2	135103	2.633	0.02	100%	275 bp	304 bp
NA12878v2-SC3	143433	2.659	0.02	100%	292 bp	324 bp

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

Sort	Group	Column	Description	ID	Scale
\|\|	SnpEff	Change rate	Change rate	`Change_rate`	None
\|\|	SnpEff	Ts/Tv	Transitions / Transversions ratio	`Ts_Tv_ratio`	None
\|\|	SnpEff	M Variants	Number of variants before filter (millions)	`Number_of_variants_before_filter`	None
\|\|	Sentieon	% Aligned	Percent of aligned reads	`PCT_PF_READS_ALIGNED`	None
\|\|	Sentieon	Insert Size	Median Insert Size, all read orientations (bp)	`summed_median`	None
\|\|	Sentieon	Mean Insert Size	Mean Insert Size, all read orientations (bp)	`summed_mean`	None

All Metrics

All metrics generated by the nf-wgs-pipeline.

All metrics generated by the nf-wgs-pipeline

Showing ³/₃ rows and ⁸⁸/₈₈ columns.

sample_name	Mean Read Length	Sampled Reads	PF Reads	Proportion PF Reads	PF Reads Aligned	Proportion PF Reads Aligned	PF Aligned Bases	PF HQ Aligned Reads	PF HQ Aligned Bases	PF HQ Aligned Q20 Bases	PF HQ Median Mismatches	PF Mismatch Rate	PF HQ Error Rate	PF Indel Rate	Reads Aligned in Pairs	Proportion Reads Aligned in Pairs	Strand Balance	Proportion Chimeras	chr1	chr2	chr3	chr4	chr5	chr6	chr7	chr8	chr9	chr10	chr11	chr12	chr13	chr14	chr15	chr16	chr17	chr18	chr19	chr20	chr21	chr22	chrX	chrY	chrM	Genome Territory	Mean Coverage	SD Coverage	Median Coverage	MAD Coverage	PCT_EXC_UNPAIRED	PCT_EXC_CAPPED	PCT_EXC_TOTAL	PCT_1X	PCT_5X	HET_SNP_SENSITIVITY	HET_SNP_Q	WINDOW_SIZE	TOTAL_CLUSTERS	ALIGNED_READS	NC GC 0-19	NC GC 20-39	NC GC 40-59	NC GC 60-79	NC GC 80-100	Median Insert Size	Median Absolute Deviation	Min Insert Size	Max Insert Size	Mean Insert Size	Standard Deviation	Read Pairs	Unpaired Reads Examined	Read Pairs Examined	Secondary Reads	Unmapped Reads	Unpaired Read Duplicates	Read Pair Duplicates	Read Pair Optical Duplicates	Proportion Duplication	Estimated Library Size	PCT_EXC_MAPQ	PCT_EXC_BASEQ	PCT_EXC_OVERLAP	AT_DROPOUT	GC_DROPOUT
NA12878v2-SC1	151	1061577200	1061577200	1.00	1059835667	1.00	155115071342	1012247265	148902436873	140288718472	1.0000	0.0084	0.0081	0.0003	1058094134	0.9984	0.5006	0.0715	0.081	0.089	0.075	0.070	0.066	0.063	0.055	0.050	0.042	0.042	0.044	0.043	0.033	0.031	0.027	0.024	0.020	0.027	0.012	0.020	0.015	0.009	0.060	0.001	0.003	2745186691	42.032	29.740	37.000	17.000	0.001	0.005	0.206	0.974	0.944	0.9540	13.0000	100	547106727	1093546373	0.63	1.11	0.96	0.38	1.73	300	83.0	2	248671763	325	135.4	501740137	3882498	634113914	46011815	4482540	2130533	100595009	5076394	0.160	1855797680	0.04	0.06	0.10	1.81	6.94
NA12878v2-SC2	151	822813331	822813331	1.00	821190005	1.00	119116461996	778735433	113628192601	106998852217	1.0000	0.0087	0.0083	0.0003	819566679	0.9980	0.5006	0.0705	0.079	0.086	0.072	0.074	0.067	0.058	0.054	0.052	0.041	0.046	0.046	0.046	0.036	0.030	0.027	0.022	0.021	0.028	0.012	0.021	0.014	0.009	0.055	0.001	0.003	2745186691	30.996	20.531	28.000	12.000	0.002	0.004	0.241	0.974	0.939	0.9514	13.0000	100	424973668	849109853	0.61	1.10	0.96	0.39	1.85	275	84.0	2	248935523	304	139.8	390053362	3108920	476606454	38087675	3486386	1475308	62610142	3746089	0.132	1738138138	0.05	0.06	0.13	1.84	6.89
NA12878v2-SC3	151	884654683	884654683	1.00	883284330	1.00	129194634102	843627421	123955349095	116846647980	1.0000	0.0084	0.0081	0.0003	881913977	0.9984	0.5005	0.0638	0.077	0.087	0.068	0.075	0.067	0.059	0.054	0.052	0.042	0.043	0.046	0.043	0.037	0.031	0.027	0.026	0.021	0.028	0.011	0.019	0.014	0.009	0.062	0.001	0.003	2745186691	34.455	23.370	31.000	14.000	0.001	0.003	0.217	0.973	0.935	0.9476	13.0000	100	454321214	908143279	0.66	1.13	0.93	0.36	1.58	293	89.0	2	248582777	324	146.9	420800286	2797884	520924336	33991635	3263716	1418678	75988641	4100188	0.147	1681193878	0.04	0.05	0.12	1.93	7.70

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

Sort	Column	Description	ID	Scale
\|\|	Mean Read Length	Mean Read Length	`MEAN_READ_LENGTH`	None
\|\|	Sampled Reads	Sampled Reads	`TOTAL_READS`	None
\|\|	PF Reads	PF Reads	`PF_READS`	None
\|\|	Proportion PF Reads	Proportion PF Reads	`PCT_PF_READS`	None
\|\|	PF Noise Reads	PF Noise Reads	`PF_NOISE_READS`	None
\|\|	PF Reads Aligned	PF Reads Aligned	`PF_READS_ALIGNED`	None
\|\|	Proportion PF Reads Aligned	Proportion PF Reads Aligned	`PCT_PF_READS_ALIGNED`	None
\|\|	PF Aligned Bases	PF Aligned Bases	`PF_ALIGNED_BASES`	None
\|\|	PF HQ Aligned Reads	PF HQ Aligned Reads	`PF_HQ_ALIGNED_READS`	None
\|\|	PF HQ Aligned Bases	PF HQ Aligned Bases	`PF_HQ_ALIGNED_BASES`	None
\|\|	PF HQ Aligned Q20 Bases	PF HQ Aligned Q20 Bases	`PF_HQ_ALIGNED_Q20_BASES`	None
\|\|	PF HQ Median Mismatches	PF HQ Median Mismatches	`PF_HQ_MEDIAN_MISMATCHES`	None
\|\|	PF Mismatch Rate	PF Mismatch Rate	`PF_MISMATCH_RATE`	None
\|\|	PF HQ Error Rate	PF HQ Error Rate	`PF_HQ_ERROR_RATE`	None
\|\|	PF Indel Rate	PF Indel Rate	`PF_INDEL_RATE`	None
\|\|	Reads Aligned in Pairs	Reads Aligned in Pairs	`READS_ALIGNED_IN_PAIRS`	None
\|\|	Proportion Reads Aligned in Pairs	Proportion Reads Aligned in Pairs	`PCT_READS_ALIGNED_IN_PAIRS`	None
\|\|	Bad Cycles	Bad Cycles	`BAD_CYCLES`	None
\|\|	Strand Balance	Strand Balance	`STRAND_BALANCE`	None
\|\|	Proportion Chimeras	Proportion Chimeras	`PCT_CHIMERAS`	None
\|\|	Proportion Adapters	Proportion Adapters	`PCT_ADAPTER`	None
\|\|	chr1	chr1	`chr1`	None
\|\|	chr2	chr2	`chr2`	None
\|\|	chr3	chr3	`chr3`	None
\|\|	chr4	chr4	`chr4`	None
\|\|	chr5	chr5	`chr5`	None
\|\|	chr6	chr6	`chr6`	None
\|\|	chr7	chr7	`chr7`	None
\|\|	chr8	chr8	`chr8`	None
\|\|	chr9	chr9	`chr9`	None
\|\|	chr10	chr10	`chr10`	None
\|\|	chr11	chr11	`chr11`	None
\|\|	chr12	chr12	`chr12`	None
\|\|	chr13	chr13	`chr13`	None
\|\|	chr14	chr14	`chr14`	None
\|\|	chr15	chr15	`chr15`	None
\|\|	chr16	chr16	`chr16`	None
\|\|	chr17	chr17	`chr17`	None
\|\|	chr18	chr18	`chr18`	None
\|\|	chr19	chr19	`chr19`	None
\|\|	chr20	chr20	`chr20`	None
\|\|	chr21	chr21	`chr21`	None
\|\|	chr22	chr22	`chr22`	None
\|\|	chrX	chrX	`chrX`	None
\|\|	chrY	chrY	`chrY`	None
\|\|	chrM	chrM	`chrM`	None
\|\|	Genome Territory	Genome Territory	`GENOME_TERRITORY`	None
\|\|	Mean Coverage	Mean Coverage	`MEAN_COVERAGE`	None
\|\|	SD Coverage	SD Coverage	`SD_COVERAGE`	None
\|\|	Median Coverage	Median Coverage	`MEDIAN_COVERAGE`	None
\|\|	MAD Coverage	MAD Coverage	`MAD_COVERAGE`	None
\|\|	PCT_EXC_UNPAIRED	The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.	`PCT_EXC_UNPAIRED`	None
\|\|	PCT_EXC_CAPPED	The fraction of aligned bases that were filtered out because they would have raised coverage above the capped value (default cap = 250x).	`PCT_EXC_CAPPED`	None
\|\|	PCT_EXC_TOTAL	The total fraction of aligned bases excluded due to all filters.	`PCT_EXC_TOTAL`	None
\|\|	PCT_1X	The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.	`PCT_1X`	None
\|\|	PCT_5X	The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.	`PCT_5X`	None
\|\|	HET_SNP_SENSITIVITY	The theoretical HET SNP sensitivity.	`HET_SNP_SENSITIVITY`	None
\|\|	HET_SNP_Q	The Phred Scaled Q Score of the theoretical HET SNP sensitivity.	`HET_SNP_Q`	None
\|\|	WINDOW_SIZE	The window size on the genome used to calculate the GC of the sequence.	`WINDOW_SIZE`	None
\|\|	TOTAL_CLUSTERS	The total number of clusters that were seen in the gc bias calculation.	`TOTAL_CLUSTERS`	None
\|\|	ALIGNED_READS	The total number of aligned reads used to compute the gc bias metrics.	`ALIGNED_READS`	None
\|\|	NC GC 0-19	Normalized coverage over quintile of GC content ranging from 0 - 19.	`GC_NC_0_19`	None
\|\|	NC GC 20-39	Normalized coverage over quintile of GC content ranging from 20 - 39.	`GC_NC_20_39`	None
\|\|	NC GC 40-59	Normalized coverage over quintile of GC content ranging from 40 - 59.	`GC_NC_40_59`	None
\|\|	NC GC 60-79	Normalized coverage over quintile of GC content ranging from 60 - 79.	`GC_NC_60_79`	None
\|\|	NC GC 80-100	Normalized coverage over quintile of GC content ranging from 80 - 100.	`GC_NC_80_100`	None
\|\|	Median Insert Size	Median Insert Size	`MEDIAN_INSERT_SIZE`	None
\|\|	Median Absolute Deviation	Median Absolute Deviation	`MEDIAN_ABSOLUTE_DEVIATION`	None
\|\|	Min Insert Size	Min Insert Size	`MIN_INSERT_SIZE`	None
\|\|	Max Insert Size	Max Insert Size	`MAX_INSERT_SIZE`	None
\|\|	Mean Insert Size	Mean Insert Size	`MEAN_INSERT_SIZE`	None
\|\|	Standard Deviation	Insert size standard deviation	`STANDARD_DEVIATION`	None
\|\|	Read Pairs	Read pairs examined for insert size estimate.	`READ_PAIRS`	None
\|\|	Unpaired Reads Examined	Unpaired Reads Examined	`UNPAIRED_READS_EXAMINED`	None
\|\|	Read Pairs Examined	Read Pairs Examined	`READ_PAIRS_EXAMINED`	None
\|\|	Secondary Reads	Secondary Reads	`SECONDARY_OR_SUPPLEMENTARY_RDS`	None
\|\|	Unmapped Reads	Unmapped Reads	`UNMAPPED_READS`	None
\|\|	Unpaired Read Duplicates	Unpaired Read Duplicates	`UNPAIRED_READ_DUPLICATES`	None
\|\|	Read Pair Duplicates	Read Pair Duplicates	`READ_PAIR_DUPLICATES`	None
\|\|	Read Pair Optical Duplicates	Read Pair Optical Duplicates	`READ_PAIR_OPTICAL_DUPLICATES`	None
\|\|	Proportion Duplication	Proportion Duplication	`PERCENT_DUPLICATION`	None
\|\|	Estimated Library Size	Estimated Library Size	`ESTIMATED_LIBRARY_SIZE`	None
\|\|	PCT_EXC_DUPE	PCT_EXC_DUPE	`PCT_EXC_DUPE`	None
\|\|	PCT_EXC_MAPQ	PCT_EXC_MAPQ	`PCT_EXC_MAPQ`	None
\|\|	PCT_EXC_BASEQ	PCT_EXC_BASEQ	`PCT_EXC_BASEQ`	None
\|\|	PCT_EXC_OVERLAP	PCT_EXC_OVERLAP	`PCT_EXC_OVERLAP`	None
\|\|	AT_DROPOUT	AT_DROPOUT	`AT_DROPOUT`	None
\|\|	GC_DROPOUT	GC_DROPOUT	`GC_DROPOUT`	None

Selected Metrics

Selected metrics are subset of all metrics that provides overview of the sample quality assessment.

Showing ³/₃ rows and ⁵/₅ columns.

sample_name	% chrM	% Chimeras	% Aligned	% Error	Insert Size
NA12878v2-SC1	0.26	7.15	99.84	0.81	300
NA12878v2-SC2	0.26	7.05	99.80	0.83	275
NA12878v2-SC3	0.26	6.38	99.84	0.81	293

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

Sort	Column	Description	ID	Scale
\|\|	% chrM	Percent of reads mapping to chrM.	`chrM`	None
\|\|	% Chimeras	Percent of reads with two ends mapping to different chromosomes or with long insert size.	`PCT_CHIMERAS`	None
\|\|	% Aligned	Percent of reads that aligned to reference genome.	`PCT_READS_ALIGNED_IN_PAIRS`	None
\|\|	% Error	Percent of bases that mismatch the reference in aligned reads.	`PF_HQ_ERROR_RATE`	None
\|\|	Insert Size	Median Insert Size estimated from sampled reads.	`MEDIAN_INSERT_SIZE`	None

SnpEff

SnpEff is a genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). .DOI: 10.4161/fly.19695.

Variants by Genomic Region

The stacked bar plot shows locations of detected variants in the genome and the number of variants for each location.

The upstream and downstream interval size to detect these genomic regions is 5000bp by default.

Variant Effects by Impact

The stacked bar plot shows the putative impact of detected variants and the number of variants for each impact.

There are four levels of impacts predicted by SnpEff:

High: High impact (like stop codon)
Moderate: Middle impact (like same type of amino acid substitution)
Low: Low impact (ie silence mutation)
Modifier: No impact

Variants by Effect Types

The stacked bar plot shows the effect of variants at protein level and the number of variants for each effect type.

This plot shows the effect of variants with respect to the mRNA.

Variants by Functional Class

The stacked bar plot shows the effect of variants and the number of variants for each effect type.

This plot shows the effect of variants on the translation of the mRNA as protein. There are three possible cases:

Silent: The amino acid does not change.
Missense: The amino acid is different.
Nonsense: The variant generates a stop codon.

Variant Qualities

The line plot shows the quantity as function of the variant quality score.

The quality score corresponds to the QUAL column of the VCF file. This score is set by the variant caller.

Sentieon

Sentieon contains a suite of QC tools. The ones represented in this module are analogues of Picard QC metrics.

Alignment Summary

Please note that Sentieon's read counts are divided by two for paired-end 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.

Insert Size

Plot shows the number of reads at a given insert size. Reads with different orientations are summed.

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BJ-WGS v1.6.0

General Statistics

General Statistics: Columns

All Metrics

Project Id Af36782F-89Fa-40Eb-B929-6Ffa07E9E16E: Columns

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SnpEff

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Sentieon

Alignment Summary

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Insert Size

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