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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

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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:

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

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

Selected Metrics

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

Showing ⁵/₅ rows and ¹⁰/₁₀ 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
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

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`

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	329.0	39513.7	4.0	329.0
C[C>T]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	11.0	329.0	33434.7	3.3	329.0
C[C>T]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	16.0	329.0	48632.2	4.9	329.0
C[T>A]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
C[T>A]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
C[T>A]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
C[T>A]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
C[T>C]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
C[T>C]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
C[T>C]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
C[T>C]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
C[T>G]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
C[T>G]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
C[T>G]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
C[T>G]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
G[C>A]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	5.0	329.0	15197.6	1.5	329.0
G[C>A]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
G[C>A]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
G[C>A]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
G[C>G]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
G[C>G]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
G[C>G]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
G[C>G]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
G[C>T]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	10.0	329.0	30395.1	3.0	329.0
G[C>T]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	3.0	329.0	9118.5	0.9	329.0
G[C>T]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	10.0	329.0	30395.1	3.0	329.0
G[C>T]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	12.0	329.0	36474.2	3.6	329.0
G[T>A]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
G[T>A]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
G[T>A]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
G[T>A]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
G[T>C]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
G[T>C]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
G[T>C]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	3.0	329.0	9118.5	0.9	329.0
G[T>C]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	3.0	329.0	9118.5	0.9	329.0
G[T>G]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
G[T>G]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
G[T>G]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
G[T>G]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
T[C>A]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
T[C>A]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
T[C>A]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
T[C>A]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
T[C>G]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
T[C>G]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
T[C>G]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
T[C>G]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
T[C>T]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	13.0	329.0	39513.7	4.0	329.0
T[C>T]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	23.0	329.0	69908.8	7.0	329.0
T[C>T]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	5.0	329.0	15197.6	1.5	329.0
T[C>T]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	23.0	329.0	69908.8	7.0	329.0
T[T>A]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	5.0	329.0	15197.6	1.5	329.0
T[T>A]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
T[T>A]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
T[T>A]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	2.0	329.0	6079.0	0.6	329.0
T[T>C]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
T[T>C]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	5.0	329.0	15197.6	1.5	329.0
T[T>C]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	4.0	329.0	12158.1	1.2	329.0
T[T>C]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	4.0	329.0	12158.1	1.2	329.0
T[T>G]A	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	0.0	329.0	0.0	0.0	329.0
T[T>G]C	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
T[T>G]G	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	1.0	329.0	3039.5	0.3	329.0
T[T>G]T	HP-AAC377GM5-SUM229-R1-SC5_S15_L001	SBS96	6.0	329.0	18237.1	1.8	329.0

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

Sort	Column	Description	ID
\|\|	SampleName	SampleName	`SampleName`
\|\|	Pattern	Pattern	`Pattern`
\|\|	Count	Count	`Count`
\|\|	Pattern_Total	Pattern_Total	`Pattern_Total`
\|\|	Normalized_Count	Normalized_Count	`Normalized_Count`
\|\|	Percentage	Percentage	`Percentage`
\|\|	Pattern_Total_Count	Pattern_Total_Count	`Pattern_Total_Count`

All Metrics

Showing ⁵/₅ rows and ⁸⁸/₈₈ columns.

Sample	CATEGORY	TOTAL_READS	PF_READS	PCT_PF_READS	PF_READS_ALIGNED	PCT_PF_READS_ALIGNED	PF_ALIGNED_BASES	PF_HQ_ALIGNED_READS	PF_HQ_ALIGNED_BASES	PF_HQ_ALIGNED_Q20_BASES	PF_HQ_MEDIAN_MISMATCHES	MEAN_READ_LENGTH	READS_ALIGNED_IN_PAIRS	PCT_READS_ALIGNED_IN_PAIRS	PF_READS_IMPROPER_PAIRS	PCT_PF_READS_IMPROPER_PAIRS	STRAND_BALANCE	PCT_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	WIDTH_OF_10_PERCENT	WIDTH_OF_20_PERCENT	WIDTH_OF_30_PERCENT	WIDTH_OF_40_PERCENT	WIDTH_OF_50_PERCENT	WIDTH_OF_60_PERCENT	WIDTH_OF_70_PERCENT	WIDTH_OF_80_PERCENT	WIDTH_OF_90_PERCENT	WIDTH_OF_95_PERCENT	WIDTH_OF_99_PERCENT	READS_USED	WINDOW_SIZE	TOTAL_CLUSTERS	ALIGNED_READS	AT_DROPOUT	GC_DROPOUT	GC_NC_0_19	GC_NC_20_39	GC_NC_40_59	GC_NC_60_79	GC_NC_80_100	GENOME_TERRITORY_bm	MEAN_COVERAGE_bm	SD_COVERAGE_bm	MEDIAN_COVERAGE_bm	MAD_COVERAGE_bm	PCT_EXC_OVERLAP_bm	PCT_EXC_TOTAL_bm	PCT_1X_bm	PCT_5X_bm	PCT_10X_bm	PCT_15X_bm	PCT_20X_bm	PCT_25X_bm	PCT_30X_bm	PCT_40X_bm	PCT_50X_bm	PCT_60X_bm	PCT_70X_bm	PCT_80X_bm	PCT_90X_bm	FOLD_80_BASE_PENALTY_bm	FOLD_90_BASE_PENALTY_bm	FOLD_95_BASE_PENALTY_bm	HET_SNP_SENSITIVITY_bm	HET_SNP_Q_bm	ADO_PERC
HP-AAC377GM5-SUM229-R1-SC5_S15_L001	PAIR	932743292	932743292	1	928765375	1.0	133972223798	892119026	129338463115	124712112484	1	149.8	926232818	1.0	106694753	0.1	0.5	0.1	300.0	250.0	82.0	2	248934684	325.9	140.7	415883154	FR	33	63	95	129	165	203	247	309	431	597	1251	ALL	100	496207079	990195300	2.2	4.1	0.6	1.0	1.0	0.5	2.8	3043453562	36.3	29.3	30	15	0.1	0.2	0.9	0.9	0.9	0.8	0.7	0.6	0.5	0.4	0.2	0.2	0.1	0.1	0.1	2.6	7.3	?	0.9	11	NA
HP-AAC377GM5-SUM229-R1-SC6_S16_L001	PAIR	714075004	714075004	1	711592084	1.0	103163986514	685946260	99890751897	96596460453	1	149.8	709961156	1.0	69149062	0.1	0.5	0.1	304.0	250.0	82.0	2	248586566	327.7	134.7	324172759	FR	33	65	97	129	165	203	249	309	425	565	1119	ALL	100	375867902	750835509	1.7	4.7	0.6	1.1	1.0	0.5	2.7	3043453562	28.3	23.2	24	12	0.1	0.2	0.9	0.9	0.8	0.7	0.6	0.5	0.4	0.2	0.1	0.1	0.1	0.0	0.0	2.6	7.1	?	0.9	10	NA
HP-AAC377GM5-SUM229-R1-SC7_S17_L001	PAIR	819169994	819169994	1	816165153	1.0	117877550299	783550376	113756077695	109891893374	1	149.8	814091868	1.0	90058165	0.1	0.5	0.1	308.0	251.0	84.0	2	248748465	333.0	143.8	367420688	FR	33	67	99	133	169	209	257	319	441	607	1309	ALL	100	434098831	866967627	2.3	3.7	0.6	1.0	1.0	0.6	3.3	3043453562	32.3	26.1	27	13	0.1	0.2	0.9	0.9	0.8	0.8	0.7	0.6	0.5	0.3	0.2	0.1	0.1	0.0	0.0	2.5	6.5	?	0.9	11	NA
HP-AAC377GM5-SUM229-R1-SC8_S18_L001	PAIR	549313510	549313510	1	546972414	1.0	79090199623	525216742	76312173066	73627996426	1	149.9	545360506	1.0	59476524	0.1	0.5	0.1	311.0	256.0	84.0	2	245448954	334.0	135.6	245737444	FR	33	65	99	133	169	209	255	317	435	573	1053	ALL	100	291139331	580923855	2.0	4.3	0.6	1.0	1.0	0.5	3.0	3043453562	21.7	18.0	18	9	0.1	0.2	0.9	0.9	0.8	0.6	0.5	0.3	0.2	0.1	0.1	0.0	0.0	0.0	0.0	2.7	7.2	?	0.9	10	NA
HP-AAC377GM5-SUM229-R1-SC9_S19_L001	PAIR	709676076	709676076	1	707064233	1.0	102466195289	680426676	99050688866	95688659900	1	150.1	705266978	1.0	76934499	0.1	0.5	0.1	311.0	261.0	78.0	2	246622693	333.6	128.8	318081395	FR	31	61	93	123	157	193	237	295	411	547	1083	ALL	100	375963340	750508344	2.7	2.9	0.6	1.0	1.0	0.6	2.7	3043453562	28.4	23.4	24	12	0.1	0.2	0.9	0.9	0.8	0.7	0.6	0.5	0.4	0.2	0.1	0.1	0.1	0.0	0.0	2.6	7.1	?	0.9	10	NA

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

Sort	Column	Description	ID
\|\|	CATEGORY	CATEGORY	`CATEGORY`
\|\|	TOTAL_READS	TOTAL_READS	`TOTAL_READS`
\|\|	PF_READS	PF_READS	`PF_READS`
\|\|	PCT_PF_READS	PCT_PF_READS	`PCT_PF_READS`
\|\|	PF_NOISE_READS	PF_NOISE_READS	`PF_NOISE_READS`
\|\|	PF_READS_ALIGNED	PF_READS_ALIGNED	`PF_READS_ALIGNED`
\|\|	PCT_PF_READS_ALIGNED	PCT_PF_READS_ALIGNED	`PCT_PF_READS_ALIGNED`
\|\|	PF_ALIGNED_BASES	PF_ALIGNED_BASES	`PF_ALIGNED_BASES`
\|\|	PF_HQ_ALIGNED_READS	PF_HQ_ALIGNED_READS	`PF_HQ_ALIGNED_READS`
\|\|	PF_HQ_ALIGNED_BASES	PF_HQ_ALIGNED_BASES	`PF_HQ_ALIGNED_BASES`
\|\|	PF_HQ_ALIGNED_Q20_BASES	PF_HQ_ALIGNED_Q20_BASES	`PF_HQ_ALIGNED_Q20_BASES`
\|\|	PF_HQ_MEDIAN_MISMATCHES	PF_HQ_MEDIAN_MISMATCHES	`PF_HQ_MEDIAN_MISMATCHES`
\|\|	PF_MISMATCH_RATE	PF_MISMATCH_RATE	`PF_MISMATCH_RATE`
\|\|	PF_HQ_ERROR_RATE	PF_HQ_ERROR_RATE	`PF_HQ_ERROR_RATE`
\|\|	PF_INDEL_RATE	PF_INDEL_RATE	`PF_INDEL_RATE`
\|\|	MEAN_READ_LENGTH	MEAN_READ_LENGTH	`MEAN_READ_LENGTH`
\|\|	READS_ALIGNED_IN_PAIRS	READS_ALIGNED_IN_PAIRS	`READS_ALIGNED_IN_PAIRS`
\|\|	PCT_READS_ALIGNED_IN_PAIRS	PCT_READS_ALIGNED_IN_PAIRS	`PCT_READS_ALIGNED_IN_PAIRS`
\|\|	PF_READS_IMPROPER_PAIRS	PF_READS_IMPROPER_PAIRS	`PF_READS_IMPROPER_PAIRS`
\|\|	PCT_PF_READS_IMPROPER_PAIRS	PCT_PF_READS_IMPROPER_PAIRS	`PCT_PF_READS_IMPROPER_PAIRS`
\|\|	BAD_CYCLES	BAD_CYCLES	`BAD_CYCLES`
\|\|	STRAND_BALANCE	STRAND_BALANCE	`STRAND_BALANCE`
\|\|	PCT_CHIMERAS	PCT_CHIMERAS	`PCT_CHIMERAS`
\|\|	PCT_ADAPTER	PCT_ADAPTER	`PCT_ADAPTER`
\|\|	MEDIAN_INSERT_SIZE	MEDIAN_INSERT_SIZE	`MEDIAN_INSERT_SIZE`
\|\|	MODE_INSERT_SIZE	MODE_INSERT_SIZE	`MODE_INSERT_SIZE`
\|\|	MEDIAN_ABSOLUTE_DEVIATION	MEDIAN_ABSOLUTE_DEVIATION	`MEDIAN_ABSOLUTE_DEVIATION`
\|\|	MIN_INSERT_SIZE	MIN_INSERT_SIZE	`MIN_INSERT_SIZE`
\|\|	MAX_INSERT_SIZE	MAX_INSERT_SIZE	`MAX_INSERT_SIZE`
\|\|	MEAN_INSERT_SIZE	MEAN_INSERT_SIZE	`MEAN_INSERT_SIZE`
\|\|	STANDARD_DEVIATION	STANDARD_DEVIATION	`STANDARD_DEVIATION`
\|\|	READ_PAIRS	READ_PAIRS	`READ_PAIRS`
\|\|	PAIR_ORIENTATION	PAIR_ORIENTATION	`PAIR_ORIENTATION`
\|\|	WIDTH_OF_10_PERCENT	WIDTH_OF_10_PERCENT	`WIDTH_OF_10_PERCENT`
\|\|	WIDTH_OF_20_PERCENT	WIDTH_OF_20_PERCENT	`WIDTH_OF_20_PERCENT`
\|\|	WIDTH_OF_30_PERCENT	WIDTH_OF_30_PERCENT	`WIDTH_OF_30_PERCENT`
\|\|	WIDTH_OF_40_PERCENT	WIDTH_OF_40_PERCENT	`WIDTH_OF_40_PERCENT`
\|\|	WIDTH_OF_50_PERCENT	WIDTH_OF_50_PERCENT	`WIDTH_OF_50_PERCENT`
\|\|	WIDTH_OF_60_PERCENT	WIDTH_OF_60_PERCENT	`WIDTH_OF_60_PERCENT`
\|\|	WIDTH_OF_70_PERCENT	WIDTH_OF_70_PERCENT	`WIDTH_OF_70_PERCENT`
\|\|	WIDTH_OF_80_PERCENT	WIDTH_OF_80_PERCENT	`WIDTH_OF_80_PERCENT`
\|\|	WIDTH_OF_90_PERCENT	WIDTH_OF_90_PERCENT	`WIDTH_OF_90_PERCENT`
\|\|	WIDTH_OF_95_PERCENT	WIDTH_OF_95_PERCENT	`WIDTH_OF_95_PERCENT`
\|\|	WIDTH_OF_99_PERCENT	WIDTH_OF_99_PERCENT	`WIDTH_OF_99_PERCENT`
\|\|	READS_USED	READS_USED	`READS_USED`
\|\|	WINDOW_SIZE	WINDOW_SIZE	`WINDOW_SIZE`
\|\|	TOTAL_CLUSTERS	TOTAL_CLUSTERS	`TOTAL_CLUSTERS`
\|\|	ALIGNED_READS	ALIGNED_READS	`ALIGNED_READS`
\|\|	AT_DROPOUT	AT_DROPOUT	`AT_DROPOUT`
\|\|	GC_DROPOUT	GC_DROPOUT	`GC_DROPOUT`
\|\|	GC_NC_0_19	GC_NC_0_19	`GC_NC_0_19`
\|\|	GC_NC_20_39	GC_NC_20_39	`GC_NC_20_39`
\|\|	GC_NC_40_59	GC_NC_40_59	`GC_NC_40_59`
\|\|	GC_NC_60_79	GC_NC_60_79	`GC_NC_60_79`
\|\|	GC_NC_80_100	GC_NC_80_100	`GC_NC_80_100`
\|\|	GENOME_TERRITORY_bm	GENOME_TERRITORY_bm	`GENOME_TERRITORY_bm`
\|\|	MEAN_COVERAGE_bm	MEAN_COVERAGE_bm	`MEAN_COVERAGE_bm`
\|\|	SD_COVERAGE_bm	SD_COVERAGE_bm	`SD_COVERAGE_bm`
\|\|	MEDIAN_COVERAGE_bm	MEDIAN_COVERAGE_bm	`MEDIAN_COVERAGE_bm`
\|\|	MAD_COVERAGE_bm	MAD_COVERAGE_bm	`MAD_COVERAGE_bm`
\|\|	PCT_EXC_ADAPTER_bm	PCT_EXC_ADAPTER_bm	`PCT_EXC_ADAPTER_bm`
\|\|	PCT_EXC_MAPQ_bm	PCT_EXC_MAPQ_bm	`PCT_EXC_MAPQ_bm`
\|\|	PCT_EXC_DUPE_bm	PCT_EXC_DUPE_bm	`PCT_EXC_DUPE_bm`
\|\|	PCT_EXC_UNPAIRED_bm	PCT_EXC_UNPAIRED_bm	`PCT_EXC_UNPAIRED_bm`
\|\|	PCT_EXC_BASEQ_bm	PCT_EXC_BASEQ_bm	`PCT_EXC_BASEQ_bm`
\|\|	PCT_EXC_OVERLAP_bm	PCT_EXC_OVERLAP_bm	`PCT_EXC_OVERLAP_bm`
\|\|	PCT_EXC_CAPPED_bm	PCT_EXC_CAPPED_bm	`PCT_EXC_CAPPED_bm`
\|\|	PCT_EXC_TOTAL_bm	PCT_EXC_TOTAL_bm	`PCT_EXC_TOTAL_bm`
\|\|	PCT_1X_bm	PCT_1X_bm	`PCT_1X_bm`
\|\|	PCT_5X_bm	PCT_5X_bm	`PCT_5X_bm`
\|\|	PCT_10X_bm	PCT_10X_bm	`PCT_10X_bm`
\|\|	PCT_15X_bm	PCT_15X_bm	`PCT_15X_bm`
\|\|	PCT_20X_bm	PCT_20X_bm	`PCT_20X_bm`
\|\|	PCT_25X_bm	PCT_25X_bm	`PCT_25X_bm`
\|\|	PCT_30X_bm	PCT_30X_bm	`PCT_30X_bm`
\|\|	PCT_40X_bm	PCT_40X_bm	`PCT_40X_bm`
\|\|	PCT_50X_bm	PCT_50X_bm	`PCT_50X_bm`
\|\|	PCT_60X_bm	PCT_60X_bm	`PCT_60X_bm`
\|\|	PCT_70X_bm	PCT_70X_bm	`PCT_70X_bm`
\|\|	PCT_80X_bm	PCT_80X_bm	`PCT_80X_bm`
\|\|	PCT_90X_bm	PCT_90X_bm	`PCT_90X_bm`
\|\|	PCT_100X_bm	PCT_100X_bm	`PCT_100X_bm`
\|\|	FOLD_80_BASE_PENALTY_bm	FOLD_80_BASE_PENALTY_bm	`FOLD_80_BASE_PENALTY_bm`
\|\|	FOLD_90_BASE_PENALTY_bm	FOLD_90_BASE_PENALTY_bm	`FOLD_90_BASE_PENALTY_bm`
\|\|	FOLD_95_BASE_PENALTY_bm	FOLD_95_BASE_PENALTY_bm	`FOLD_95_BASE_PENALTY_bm`
\|\|	HET_SNP_SENSITIVITY_bm	HET_SNP_SENSITIVITY_bm	`HET_SNP_SENSITIVITY_bm`
\|\|	HET_SNP_Q_bm	HET_SNP_Q_bm	`HET_SNP_Q_bm`
\|\|	ADO_PERC	ADO_PERC	`ADO_PERC`

Picard

Tools for manipulating high-throughput sequencing data.URL: http://broadinstitute.github.io/picard

Alignment Summary

Please note that Picard's read counts are divided by two for paired-end data. Total bases (including unaligned) is not provided.

Created with MultiQC

Mean read length

The mean read length of the set of reads examined.

Created with MultiQC

Base Distribution

Plot shows the distribution of bases by cycle.

Created with MultiQC

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.

Created with MultiQC

Insert Size

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

Created with MultiQC

Mean Base Quality by Cycle

Plot shows the mean base quality by cycle.

This metric gives an overall snapshot of sequencing machine performance. For most types of sequencing data, the output is expected to show a slight reduction in overall base quality scores towards the end of each read.

Spikes in quality within reads are not expected and may indicate that technical problems occurred during sequencing.

Created with MultiQC

Base Quality Distribution

Plot shows the count of each base quality score.

Created with MultiQC

WGS Coverage

The number of bases in the genome territory for each fold coverage. Note that final 1% of data is hidden to prevent very long tails.

Created with MultiQC

WGS Filtered Bases

For more information about the filtered categories, see the Picard documentation.

Created with MultiQC

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Pipeline	Software	Version
BJ-Parabricks-SomaticVariantCalling	DeepVariant	`1.8.0`
	Parabricks	`4.4.0`

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BJ-Parabricks-SomaticVariantCalling v1.0.0

Selected Metrics

Selected Metrics: Columns

Mutational Signature Profile

Merged Mutationalcatalog

Merged Mutationalcatalog: Columns

All Metrics

All Metrics: Columns

Picard

Alignment Summary

Mean read length

Base Distribution

GC Coverage Bias

Insert Size

Mean Base Quality by Cycle Help

Base Quality Distribution

WGS Coverage

WGS Filtered Bases

Software Versions

v1.28

Highlight Samples

Rename Samples

Show / Hide Samples

Mean Base Quality by Cycle