MultiQC Report

v1.28

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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 1.28

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-SomaticVariantCalling v1.0.0

The report aggregates all metrics from Somatic Variant analyses.

session_id: b41c7845-2f8e-4353-9639-3909ac29a389
mode: wgs
genome: GRCh38
platform: Illumina
deepvariant_model: bioskrybv1
skip_subsampling: True
skip_somatic_filter: False
skip_sigprofile: False

Report generated on 2025-05-12, 21:47 UTC

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
HP-AAC377GM5-SUM229-R1-SC5_S15_L001	932743292	1.00	0.01	149.79	1.00	0.14	300.00	325.87	2.25	4.08
HP-AAC377GM5-SUM229-R1-SC6_S16_L001	714075004	1.00	0.01	149.83	1.00	0.12	304.00	327.67	1.65	4.71
HP-AAC377GM5-SUM229-R1-SC7_S17_L001	819169994	1.00	0.01	149.78	1.00	0.13	308.00	332.97	2.30	3.68
HP-AAC377GM5-SUM229-R1-SC8_S18_L001	549313510	1.00	0.01	149.93	1.00	0.13	311.00	333.96	2.00	4.28
HP-AAC377GM5-SUM229-R1-SC9_S19_L001	709676076	1.00	0.01	150.09	1.00	0.13	311.00	333.59	2.66	2.91

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`

Mutational Signature Profile

Merged Mutationalcatalog

Showing ⁹⁶/₉₆ rows and ⁷/₇ columns.

MutationType	SampleName	Pattern	Count	Pattern_Total	Normalized_Count	Percentage	Pattern_Total_Count
A[C>A]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
A[C>A]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
A[C>A]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
A[C>A]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
A[C>G]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	3.0	329.0	9118.5	0.9	329.0
A[C>G]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	4.0	329.0	12158.1	1.2	329.0
A[C>G]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
A[C>G]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	6.0	329.0	18237.1	1.8	329.0
A[C>T]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	16.0	329.0	48632.2	4.9	329.0
A[C>T]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	14.0	329.0	42553.2	4.3	329.0
A[C>T]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	13.0	329.0	39513.7	4.0	329.0
A[C>T]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	16.0	329.0	48632.2	4.9	329.0
A[T>A]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
A[T>A]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
A[T>A]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
A[T>A]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
A[T>C]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
A[T>C]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	3.0	329.0	9118.5	0.9	329.0
A[T>C]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	5.0	329.0	15197.6	1.5	329.0
A[T>C]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
A[T>G]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	3.0	329.0	9118.5	0.9	329.0
A[T>G]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
A[T>G]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
A[T>G]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
C[C>A]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
C[C>A]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
C[C>A]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
C[C>A]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
C[C>G]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
C[C>G]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
C[C>G]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
C[C>G]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
C[C>T]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	14.0	329.0	42553.2	4.3	329.0
C[C>T]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	13.0

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