Toolbox

MultiQC Toolbox

Highlight Samples

Regex mode off

Rename Samples

Click here for bulk input.

Paste two columns of a tab-delimited table here (eg. from Excel).

First column should be the old name, second column the new name.

Regex mode off

Show / Hide Samples

Regex mode off

Explain with AI

Configure AI settings to get explanations of plots and data in this report.

Anonymize samples off

Aspect ratio

Plot scaling

Download the raw data used to create the plots in this report below:

Format:

Note that additional data was saved in multiqc_data when this report was generated.

Choose Plots

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

Settings are automatically saved. You can also save named configurations below.

Save Settings

You can save the toolbox settings for this report to the browser or as a file.

Load Settings

Choose a saved report profile from the browser or load from a file:

Tool Citations

Please remember to cite the tools that you use in your analysis.

To help with this, you can download publication details of the tools mentioned in this report:

About MultiQC

This report was generated using MultiQC, version 1.28

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/MultiQC/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

MultiQC is developed by:

BJ-Parabricks-GermlineVariantCalling v1.0.0

The report aggregates all metrics from Germline Variant analyses.

session_id: 0f26e7ad-35e6-40ce-b3f8-cc891a0fa2ae
mode: wgs
genome: GRCh38
platform: Illumina
deepvariant_model: bioskrybv1
skip_subsampling: True
skip_sigprofile: False

JavaScript Disabled

MultiQC reports use JavaScript for plots and toolbox functions. It looks like you have JavaScript disabled in your web browser. Please note that many of the report functions will not work as intended.

Report generated on 2025-05-30, 09:22 UTC

Selected Metrics

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

Showing ⁸/₈ rows and ¹¹/₁₁ columns.

Sample	PF_READS	PCT_PF_READS_ALIGNED	PF_HQ_ERROR_RATE	MEAN_READ_LENGTH	PCT_READS_ALIGNED_IN_PAIRS	PCT_CHIMERAS	MEDIAN_INSERT_SIZE	MEAN_INSERT_SIZE	AT_DROPOUT	GC_DROPOUT	ADO Percentage
ResolveDNA-v2-Auto-SC08D	635648076	0.99	0.01	151.00	1.00	0.09	307.00	327.91	2.00	7.08	0.88
ResolveDNA-v2-Auto-SC09A	756935356	1.00	0.01	151.00	1.00	0.08	286.00	306.86	1.90	5.76	0.92
ResolveDNA-v2-Manual-SC2F	876563478	0.99	0.01	151.00	1.00	0.09	302.00	323.00	2.06	5.68	0.95
ResolveDNA-v2-Manual-SC3G	983491746	0.99	0.01	151.00	1.00	0.09	305.00	324.93	2.00	5.63	NA
ResolveOME-DNA-SC3	997295300	0.99	0.01	150.22	1.00	0.15	326.00	346.71	3.92	1.70	0.96
ResolveOME-DNA-SC6	760966474	0.99	0.01	150.24	0.99	0.16	404.00	436.23	2.79	2.64	0.96
ResolveOMEv2.1-DNA-04C	869002984	1.00	0.00	150.00	1.00	0.09	350.00	368.45	0.59	3.53	0.87
ResolveOMEv2.1-DNA-08B	944212550	1.00	0.00	150.00	1.00	0.09	359.00	378.75	0.37	3.87	0.92

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

Sort	Column	Description	ID
\|\|	PF_READS	AlignmentStat: The number of PF reads where PF is defined as passing Illumina's filter.	`PF_READS`
\|\|	PCT_PF_READS_ALIGNED	AlignmentStat: The percentage of PF reads that aligned to the reference sequence. PF_READS_ALIGNED / PF_READS	`PCT_PF_READS_ALIGNED`
\|\|	PF_HQ_ERROR_RATE	AlignmentStat: The fraction of bases that mismatch the reference in PF HQ aligned reads.	`PF_HQ_ERROR_RATE`
\|\|	MEAN_READ_LENGTH	AlignmentStat: The mean read length of the set of reads examined. When looking at the data for a single lane with equal length reads this number is just the read length. When looking at data for merged lanes with differing read lengths this is the mean read length of all reads.	`MEAN_READ_LENGTH`
\|\|	PCT_READS_ALIGNED_IN_PAIRS	AlignmentStat: The fraction of reads whose mate pair was also aligned to the reference. READS_ALIGNED_IN_PAIRS / PF_READS_ALIGNED	`PCT_READS_ALIGNED_IN_PAIRS`
\|\|	PCT_CHIMERAS	AlignmentStat: The fraction of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes.	`PCT_CHIMERAS`
\|\|	MEDIAN_INSERT_SIZE	InsertSizeMetricAlgo: The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.	`MEDIAN_INSERT_SIZE`
\|\|	MEAN_INSERT_SIZE	InsertSizeMetricAlgo: The mean insert size of the 'core' of the distribution. Artefactual outliers in the distribution often cause calculation of nonsensical mean and stdev values. To avoid this the distribution is first trimmed to a 'core' distribution of +/- N median absolute deviations around the median insert size. By default N=10, but this is configurable.	`MEAN_INSERT_SIZE`
\|\|	AT_DROPOUT	GCBias: Illumina-style AT dropout metric. Calculated by taking each GC bin independently and calculating (%ref_at_gc - %reads_at_gc) and summing all positive values for GC=[0..50].	`AT_DROPOUT`
\|\|	GC_DROPOUT	GCBias: Illumina-style GC dropout metric. Calculated by taking each GC bin independently and calculating (%ref_at_gc - %reads_at_gc) and summing all positive values for GC=[50..100].	`GC_DROPOUT`
\|\|	ADO Percentage	Percentage of alleles in between 20-80%	`ADO_PERC`

All Metrics

All metrics generated by the nf-parabricks-germline pipeline.

Showing ⁸/₈ rows and ⁶⁹/₆₉ columns.

Sample	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	Total Reads After Dedup	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	Mean Read Length	Reads Aligned in Pairs	Proportion Reads Aligned in Pairs	PF Reads Improper Pairs	Proportion PF Reads Improper Pairs	Strand Balance	Proportion Chimeras	Median Insert Size	Mode Insert Size	Median Absolute Deviation	Min Insert Size	Max Insert Size	Mean Insert Size	Standard Deviation	Read Pairs	Pair Orientation	Genome Territory	Mean Coverage	SD Coverage	Median Coverage	MAD Coverage	Proportion Bases with low MAPQ	Proportion Bases with Duplicates	Proportion Bases Unpaired	Proportion Bases with low BASEQ	Proportion Bases with Overlap	Proportion Bases above Capped	Proportion Bases Excluded in Total	Proportion Bases > 1x	Proportion Bases > 5x	HET SNP Sensitivity	HET SNP Phred Scaled Q Score	Window Size on the genome	Total Clusters seen in GC Bias	Reads Used by GC Bias Algo	AT Dropout	GC Dropout	NC GC 0-19	NC GC 20-39	NC GC 40-59	NC GC 60-79	NC GC 80-100	ADO Percentage
ResolveDNA-v2-Auto-SC08D	2683431	314865329	28858399	3233987	1230784	35746501	1859258	0.115	1339235325	635648076	635648076	1.00	632414089	0.99	92129771756	593227689	87161539079	84120901424	1.0000	0.0084	0.0078	0.0004	151	629730658	0.9958	47097205	0.0745	0.5029	0.0881	307	263	78.0	2	248582949	328	126.8	261290432	FR	3043453562	22.004	17.905	19.000	10.000	0.062	0.106	0.002	0.027	0.080	0.011	0.287	0.926	0.865	0.8958	10.0000	100	331888775	661272488	2.00	7.08	0.61	1.09	0.97	0.36	6.63	0.9
ResolveDNA-v2-Auto-SC09A	2787303	375404153	31006140	3339747	1430585	46911652	2361286	0.126	1434844747	756935356	756935356	1.00	753595609	1.00	109563278055	714644654	104604312397	100888996544	1.0000	0.0083	0.0078	0.0004	151	750808306	0.9963	47403881	0.0629	0.5026	0.0764	286	238	76.0	2	248588848	307	125.4	310968008	FR	3043453562	25.247	20.303	21.000	11.000	0.051	0.119	0.001	0.027	0.101	0.010	0.311	0.929	0.884	0.9072	10.0000	100	393748887	784601749	1.90	5.76	0.57	1.06	1.00	0.42	6.02	0.9
ResolveDNA-v2-Manual-SC2F	4131428	433951836	40656280	4528378	2030832	49546703	2283323	0.116	1824588595	876563478	876563478	1.00	872035100	0.99	126677728996	823355650	120683859686	116340716958	1.0000	0.0084	0.0079	0.0004	151	867903672	0.9953	64141842	0.0736	0.5032	0.0886	302	252	76.0	2	246710324	323	124.4	360305516	FR	3043453562	30.135	22.689	27.000	13.000	0.054	0.108	0.002	0.028	0.082	0.015	0.290	0.932	0.898	0.9147	11.0000	100	458469024	912691380	2.06	5.68	0.58	1.04	1.01	0.41	7.21	0.9
ResolveDNA-v2-Manual-SC3G	4741845	486594222	48261309	5561457	2570194	64061342	3348236	0.134	1758496457	983491746	983491746	1.00	977930289	0.99	141573124913	922385225	134832740771	129719315611	1.0000	0.0087	0.0081	0.0004	151	973188444	0.9952	73784185	0.0754	0.5032	0.0920	305	267	79.0	2	248583517	325	128.9	395069323	FR	3043453562	32.818	26.166	28.000	15.000	0.054	0.124	0.002	0.029	0.081	0.018	0.309	0.929	0.892	0.9107	10.0000	100	515648508	1026191598	2.00	5.63	0.59	1.04	1.02	0.40	7.11	NA
ResolveOME-DNA-SC3	4460539	493654568	66470831	5525625	2268709	81965244	3757283	0.168	1366307905	997295300	997295300	1.00	991769675	0.99	143440751370	946349131	137575184639	133527470222	1.0000	0.0069	0.0066	0.0003	150	987309136	0.9955	123134789	0.1242	0.5021	0.1453	326	279	79.0	2	248672222	347	131.7	364516964	FR	3043453562	34.503	24.565	31.000	13.000	0.047	0.156	0.002	0.022	0.057	0.004	0.286	0.932	0.915	0.9226	11.0000	100	531313326	1058240506	3.92	1.70	0.49	0.95	1.07	0.74	6.14	1.0
ResolveOME-DNA-SC6	4754051	375407909	44030435	5396605	2385804	94057991	2808138	0.252	630652978	760966474	760966474	1.00	755569869	0.99	109260340412	718492671	104486840501	100644138475	1.0000	0.0082	0.0079	0.0003	150	750815818	0.9937	99580037	0.1318	0.5029	0.1572	404	326	113.0	2	248676812	436	180.8	243627133	FR	3043453562	24.191	16.494	22.000	9.000	0.049	0.236	0.003	0.023	0.027	0.004	0.341	0.930	0.903	0.9145	11.0000	100	402332919	799600304	2.79	2.64	0.52	0.99	1.04	0.69	7.31	1.0
ResolveOMEv2.1-DNA-04C	1933456	432288211	40552303	2493106	882437	88609596	22179075	0.206	1125153739	869002984	869002984	1.00	866509878	1.00	125464650533	812937168	118638331752	115891605057	0.0000	0.0049	0.0043	0.0004	150	864576422	0.9978	60385594	0.0697	0.5010	0.0890	350	314	78.0	2	248583752	368	133.0	321839353	FR	3043453562	28.436	18.553	27.000	11.000	0.061	0.196	0.001	0.015	0.038	0.012	0.323	0.935	0.911	0.9216	11.0000	100	455573093	907062181	0.59	3.53	0.86	1.04	1.00	0.62	3.12	0.9
ResolveOMEv2.1-DNA-08B	2458707	469225235	43929263	3303373	1164930	103569159	27747843	0.221	1133465797	944212550	944212550	1.00	940909177	1.00	136301692534	882548894	128909216874	125724472875	0.0000	0.0052	0.0045	0.0004	150	938450470	0.9974	67733753	0.0720	0.5011	0.0904	359	323	78.0	2	248583754	379	133.4	341631328	FR	3043453562	30.528	18.290	30.000	11.000	0.061	0.211	0.001	0.016	0.030	0.012	0.331	0.936	0.919	0.9271	11.0000	100	494977175	984838440	0.37	3.87	0.87	1.05	0.99	0.60	3.16	0.9

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: PROJECT_ID_PLOT_TITLE-1_table

Sort	Column	Description	ID
\|\|	Unpaired Reads Examined	Picard DuplicationMetrics: The number of mapped reads examined which did not have a mapped mate pair, either because the read is unpaired, or the read is paired to an unmapped mate.	`UNPAIRED_READS_EXAMINED`
\|\|	Read Pairs Examined	Picard DuplicationMetrics: The number of mapped read pairs examined. (Primary, non-supplemental)	`READ_PAIRS_EXAMINED`
\|\|	Secondary Reads	Picard DuplicationMetrics: The number of reads that were either secondary or supplementary	`SECONDARY_OR_SUPPLEMENTARY_RDS`
\|\|	Unmapped Reads	Picard DuplicationMetrics: The total number of unmapped reads examined. (Primary, non-supplemental)	`UNMAPPED_READS`
\|\|	Unpaired Read Duplicates	Picard DuplicationMetrics: The number of fragments that were marked as duplicates.	`UNPAIRED_READ_DUPLICATES`
\|\|	Read Pair Duplicates	Picard DuplicationMetrics: The number of read pairs that were marked as duplicates.	`READ_PAIR_DUPLICATES`
\|\|	Read Pair Optical Duplicates	Picard DuplicationMetrics: The number of read pairs duplicates that were caused by optical duplication. Value is always < READ_PAIR_DUPLICATES, which counts all duplicates regardless of source.	`READ_PAIR_OPTICAL_DUPLICATES`
\|\|	Proportion Duplication	Picard DuplicationMetrics: The fraction of mapped sequence that is marked as duplicate.	`PERCENT_DUPLICATION`
\|\|	Estimated Library Size	Picard DuplicationMetrics: The estimated number of unique molecules in the library based on PE duplication.	`ESTIMATED_LIBRARY_SIZE`
\|\|	Total Reads After Dedup	AlignmentStat: The total number of reads including all PF and non-PF reads. When CATEGORY equals PAIR this value will be 2x the number of clusters.	`TOTAL_READS`
\|\|	PF Reads	AlignmentStat: The number of PF reads where PF is defined as passing Illumina's filter.	`PF_READS`
\|\|	Proportion PF Reads	AlignmentStat: The fraction of reads that are PF (PF_READS / TOTAL_READS)	`PCT_PF_READS`
\|\|	PF Noise Reads	AlignmentStat: The number of PF reads that are marked as noise reads. A noise read is one which is composed entirely of A bases and/or N bases. These reads are marked as they are usually artifactual and are of no use in downstream analysis.	`PF_NOISE_READS`
\|\|	PF Reads Aligned	AlignmentStat: The number of PF reads that were aligned to the reference sequence. This includes reads that aligned with low quality (i.e. their alignments are ambiguous).	`PF_READS_ALIGNED`
\|\|	Proportion PF Reads Aligned	AlignmentStat: The percentage of PF reads that aligned to the reference sequence. PF_READS_ALIGNED / PF_READS	`PCT_PF_READS_ALIGNED`
\|\|	PF Aligned Bases	AlignmentStat: The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence.	`PF_ALIGNED_BASES`
\|\|	PF HQ Aligned Reads	AlignmentStat: The number of PF reads that were aligned to the reference sequence with a mapping quality of Q20 or higher signifying that the aligner estimates a 1/100 (or smaller) chance that the alignment is wrong.	`PF_HQ_ALIGNED_READS`
\|\|	PF HQ Aligned Bases	AlignmentStat: The number of bases aligned to the reference sequence in reads that were mapped at high quality. Will usually approximate PF_HQ_ALIGNED_READS * READ_LENGTH but may differ when either mixed read lengths are present or many reads are aligned with gaps.	`PF_HQ_ALIGNED_BASES`
\|\|	PF HQ Aligned Q20 Bases	AlignmentStat: The number of bases aligned to the reference sequence in reads that were mapped at high quality. Will usually approximate PF_HQ_ALIGNED_READS * READ_LENGTH but may differ when either mixed read lengths are present or many reads are aligned with gaps.	`PF_HQ_ALIGNED_Q20_BASES`
\|\|	PF HQ Median Mismatches	AlignmentStat: The median number of mismatches versus the reference sequence in reads that were aligned to the reference at high quality (i.e. PF_HQ_ALIGNED READS).	`PF_HQ_MEDIAN_MISMATCHES`
\|\|	PF Mismatch Rate	AlignmentStat: The rate of bases mismatching the reference for all bases aligned to the reference sequence.	`PF_MISMATCH_RATE`
\|\|	PF HQ Error Rate	AlignmentStat: The fraction of bases that mismatch the reference in PF HQ aligned reads.	`PF_HQ_ERROR_RATE`
\|\|	PF Indel Rate	AlignmentStat: The number of insertion and deletion events per 100 aligned bases. Uses the number of events as the numerator, not the number of inserted or deleted bases.	`PF_INDEL_RATE`
\|\|	Mean Read Length	AlignmentStat: The mean read length of the set of reads examined. When looking at the data for a single lane with equal length reads this number is just the read length. When looking at data for merged lanes with differing read lengths this is the mean read length of all reads.	`MEAN_READ_LENGTH`
\|\|	Reads Aligned in Pairs	AlignmentStat: The number of aligned reads whose mate pair was also aligned to the reference.	`READS_ALIGNED_IN_PAIRS`
\|\|	Proportion Reads Aligned in Pairs	AlignmentStat: The fraction of reads whose mate pair was also aligned to the reference. READS_ALIGNED_IN_PAIRS / PF_READS_ALIGNED	`PCT_READS_ALIGNED_IN_PAIRS`
\|\|	PF Reads Improper Pairs	AlignmentStat: The number of PF reads that were aligned to the reference sequence but whose mate pair was not aligned to the reference sequence.	`PF_READS_IMPROPER_PAIRS`
\|\|	Proportion PF Reads Improper Pairs	AlignmentStat: The fraction of PF reads that were aligned to the reference sequence but whose mate pair was not aligned to the reference sequence.	`PCT_PF_READS_IMPROPER_PAIRS`
\|\|	Bad Cycles	AlignmentStat: The number of instrument cycles in which 80% or more of base calls were no-calls.	`BAD_CYCLES`
\|\|	Strand Balance	AlignmentStat: The number of PF reads aligned to the positive strand of the genome divided by the number of PF reads aligned to the genome.	`STRAND_BALANCE`
\|\|	Proportion Chimeras	AlignmentStat: The fraction of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes.	`PCT_CHIMERAS`
\|\|	Proportion Adapters	AlignmentStat: The fraction of PF reads that are unaligned and match to a known adapter sequence right from the start of the read.	`PCT_ADAPTER`
\|\|	Median Insert Size	InsertSizeMetricAlgo: The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.	`MEDIAN_INSERT_SIZE`
\|\|

Toggle navigation v1.28

MultiQC Toolbox

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Explain with AI

Export Plots

Choose Plots

Save Settings

Load Settings

Tool Citations

About MultiQC

BJ-Parabricks-GermlineVariantCalling v1.0.0

Selected Metrics

Selected Metrics: Columns

All Metrics

All Metrics: Columns

v1.28

Highlight Samples

Rename Samples

Show / Hide Samples