MultiQC Report

General Statistics

Showing ²/₂ rows and ¹¹/₁₁ columns.

Sample Name	Alignments	Reads	Mapped Reads	Properly Paired Reads	Duplicate Reads	Contamination	Ploidy	Purity	QC PURPLE	QC AMBER	Gender
HCC1395 HCC1395.normal_dna	890M	871M	99.65%	98.68%	2.04%
HCC1395 HCC1395.tumor_dna	1808M	1765M	99.63%	98.72%	3.69%	0.00%	2.8200	100.00%	Pass	Pass	Male

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

Sort	Group	Column	Description	ID
\|\|	BamTools	Alignments	Total number of alignments including both reads that passed QC and reads that failed QC	`bamtools-flag_counts_alignments_total`
\|\|	BamTools	Reads	Total number of primary reads (reads that passed QC only)	`bamtools-flag_counts_reads_total`
\|\|	BamTools	Mapped Reads	Percentage of primary reads that mapped to the reference genome	`bamtools-flag_counts_reads_mapped_pct`
\|\|	BamTools	Properly Paired Reads	Percentage of reads mapped in a proper pair: correct orientation and insert size (SAM flag 0x2)	`bamtools-flag_counts_reads_pp_pct`
\|\|	BamTools	Duplicate Reads	Percentage of primary reads marked as PCR or optical duplicates (SAM flag 0x400)	`bamtools-flag_counts_reads_dup_pct`
\|\|	AMBER	Contamination	Estimated percentage of cross sample contamination detected via B allele frequency shifts at homozygous reference sites	`amber-qc_contamination`
\|\|	PURPLE	Ploidy	Average copy number of the tumor genome (diploid = 2; tetraploid of ~4)	`purple-purity_ploidy`
\|\|	PURPLE	Purity	Estimated tumor cell fraction: the proportion of cells in the sample that are tumor derived	`purple-purity_purity`
\|\|	PURPLE	QC PURPLE	Overall PURPLE QC status: PASS or FAIL based on quality metrics and solution reliability	`purple-qc_status`
\|\|	AMBER	QC AMBER	Overall AMBER QC status (PASS or FAIL) based on contamination and BAF quality thresholds	`amber-qc_status`
\|\|	PURPLE	Gender	Predicted sex of the patient based on somatic copy number profile of sex chromosomes	`purple-purity_gender`

AMBER

https://github.com/hartwigmedical/hmftools/tree/master/amber

Showing ²/₂ rows and ⁵/₇ columns.

Sample Name	Status	Consanguinity Proportion	Contamination	Contamination Sites	Homozygous Regions Pass	Homozygous Regions Total	Uniparental Disomy
HCC1395 HCC1395.normal_dna					1	51
HCC1395 HCC1395.tumor_dna	Pass	0.11%	0.00%	86038			NONE

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: table-1437684_table

Sort	Column	Description	ID
\|\|	Status	Overall AMBER QC status (PASS or FAIL) based on contamination and BAF quality thresholds	`qc_status`
\|\|	Consanguinity Proportion	Proportion of the genome in long runs of homozygosity; elevated values suggest related parents or population inbreeding	`qc_consanguinity_proportion`
\|\|	Contamination	Estimated percentage of cross sample contamination detected via B allele frequency shifts at homozygous reference sites	`qc_contamination`
\|\|	Contamination Sites	Number of homozygous reference SNP sites in the normal sample evaluated for cross sample contamination in the tumor	`contamination_sites_count`
\|\|	Homozygous Regions Pass	Number of homozygous regions passing QC filters; used to assess consanguinity and uniparental disomy	`homozygousregions_pass`
\|\|	Homozygous Regions Total	Total number of long homozygous stretches detected in the reference sample genome	`homozygousregions_total`
\|\|	Uniparental Disomy	Detection of uniparental disomy (both copies of a chromosome inherited from one parent), inferred from homozygous regions restricted to specific chromosomes	`qc_uniparental_disomy`

BamTools

https://github.com/hartwigmedical/hmftools/tree/master/bam-tools

Summary

Showing ²/₂ rows and ²⁸/₂₈ columns.

Sample Name	Total Region Bases	Total Reads	Duplicate Reads	Dual Strand Reads	Mean Coverage	Std Dev Coverage	Median Coverage	MAD Coverage	Low Map Qual	Duplicate	Unmapped	Low Base Qual	Overlapping Read	Capped Coverage	Depth Coverage 1	Depth Coverage 5	Depth Coverage 10	Depth Coverage 15	Depth Coverage 20	Depth Coverage 25	Depth Coverage 30	Depth Coverage 40	Depth Coverage 50	Depth Coverage 60	Depth Coverage 70	Depth Coverage 80	Depth Coverage 90	Depth Coverage 100
HCC1395 HCC1395.normal_dna	2923M	873M	18M	0M	40.96	14.18	43.00	8.00	3.59%	1.97%	0.24%	0.30%	1.03%	0.01%	97.29%	96.70%	96.22%	95.15%	92.41%	87.86%	82.26%	61.90%	26.82%	5.07%	0.57%	0.19%	0.13%	0.09%
HCC1395 HCC1395.tumor_dna	2923M	1769M	65M	0M	80.67	39.55	75.00	22.00	3.94%	3.56%	0.26%	0.28%	1.53%	0.10%	96.83%	96.25%	95.99%	95.73%	95.33%	94.54%	93.20%	89.28%	83.07%	71.24%	56.47%	44.57%	35.31%	27.20%

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: table-9852111_table

Sort	Column	Description	ID
\|\|	Total Region Bases	Total number of non N reference bases in the assessed genome territory over which coverage is calculated	`summary_total_region_bases`
\|\|	Total Reads	Total number of primary reads passing QC filters used for coverage calculation	`summary_total_reads`
\|\|	Duplicate Reads	Number of reads marked as duplicates (PCR or optical) excluded from coverage if duplicate filtering is enabled	`summary_duplicate_reads`
\|\|	Dual Strand Reads	Number of reads where both forward and reverse strands contributed coverage at the same position	`summary_dual_strand_reads`
\|\|	Mean Coverage	Mean depth of coverage across the genome territory after applying all base quality and mapping quality filters	`summary_mean_coverage`
\|\|	Std Dev Coverage	Standard deviation of coverage depth across the genome territory	`summary_std_dev_coverage`
\|\|	Median Coverage	Median depth of coverage: 50th percentile of per base coverage across the genome territory	`summary_median_coverage`
\|\|	MAD Coverage	Median absolute deviation of coverage: a robust measure of coverage dispersion, less sensitive to outliers than standard deviation	`summary_mad_coverage`
\|\|	Low Map Qual	Percentage of aligned bases filtered due to low mapping quality (default threshold: MAPQ < 20)	`summary_low_map_qual_percent`
\|\|	Duplicate	Percentage of aligned bases filtered because they were in reads marked as duplicates	`summary_duplicate_percent`
\|\|	Unmapped	Percentage of aligned bases filtered because they were in unmapped reads or reads with unmapped mates	`summary_unmapped_percent`
\|\|	Low Base Qual	Percentage of aligned bases filtered due to low base quality (default threshold: base quality < 20)	`summary_low_base_qual_percent`
\|\|	Overlapping Read	Percentage of aligned bases filtered from the second read of overlapping pairs to avoid double counting	`summary_overlapping_read_percent`
\|\|	Capped Coverage	Percentage of aligned bases filtered because coverage exceeded the cap threshold (default 250x)	`summary_capped_coverage`
\|\|	Depth Coverage 1	Percentage of genome territory bases covered at ≥1x depth	`summary_depth_coverage_1`
\|\|	Depth Coverage 5	Percentage of genome territory bases covered at ≥5× depth	`summary_depth_coverage_5`
\|\|	Depth Coverage 10	Percentage of genome territory bases covered at ≥10× depth	`summary_depth_coverage_10`
\|\|	Depth Coverage 15	Percentage of genome territory bases covered at ≥15× depth	`summary_depth_coverage_15`
\|\|	Depth Coverage 20	Percentage of genome territory bases covered at ≥20× depth	`summary_depth_coverage_20`
\|\|	Depth Coverage 25	Percentage of genome territory bases covered at ≥25× depth	`summary_depth_coverage_25`
\|\|	Depth Coverage 30	Percentage of genome territory bases covered at ≥30× depth; clinical WGS coverage threshold	`summary_depth_coverage_30`
\|\|	Depth Coverage 40	Percentage of genome territory bases covered at ≥40× depth	`summary_depth_coverage_40`
\|\|	Depth Coverage 50	Percentage of genome territory bases covered at ≥50× depth	`summary_depth_coverage_50`
\|\|	Depth Coverage 60	Percentage of genome territory bases covered at ≥60× depth	`summary_depth_coverage_60`
\|\|	Depth Coverage 70	Percentage of genome territory bases covered at ≥70× depth	`summary_depth_coverage_70`
\|\|	Depth Coverage 80	Percentage of genome territory bases covered at ≥80× depth	`summary_depth_coverage_80`
\|\|	Depth Coverage 90	Percentage of genome territory bases covered at ≥90× depth	`summary_depth_coverage_90`
\|\|	Depth Coverage 100	Percentage of genome territory bases covered at ≥100× depth	`summary_depth_coverage_100`

Flag Statistics

Showing ²/₂ rows and ¹⁹/₁₉ columns.

Sample Name	Alignments	Reads	Mapped Reads	Duplicate Reads	Properly Paired Reads	Secondary	Supplementary	Duplicate	Primary Duplicate	Mapped	Primary Mapped	Paired	Read 1	Read 2	Properly Paired	Properly Paired Mate Mapped	Singleton	Mate Diff Chrm	Mate Diff Chrm MAPQ≥5
HCC1395 HCC1395.normal_dna	890M	871M	99.65%	2.04%	98.68%	0	1979194	18M	18M	870M	868M	871M	436M	436M	860M	865M	3010578	2525957	1510216
HCC1395 HCC1395.tumor_dna	1808M	1765M	99.63%	3.69%	98.72%	0	4114394	65M	65M	1763M	1759M	1765M	883M	883M	1743M	1752M	6515982	4700156	2698508

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: table-2208516_table

Sort	Column	Description	ID
\|\|	Alignments	Total number of alignments including both reads that passed QC and reads that failed QC	`flag_counts_alignments_total`
\|\|	Reads	Total number of primary reads (reads that passed QC only)	`flag_counts_reads_total`
\|\|	Mapped Reads	Percentage of primary reads that mapped to the reference genome	`flag_counts_reads_mapped_pct`
\|\|	Duplicate Reads	Percentage of primary reads marked as PCR or optical duplicates (SAM flag 0x400)	`flag_counts_reads_dup_pct`
\|\|	Properly Paired Reads	Percentage of reads mapped in a proper pair: correct orientation and insert size (SAM flag 0x2)	`flag_counts_reads_pp_pct`
\|\|	Secondary	Number of secondary (alternative) alignments for multimapping reads (SAM flag 0x100)	`flag_counts_secondary_pass`
\|\|	Supplementary	Number of supplementary alignments: chimeric or split read segments mapping to different loci (SAM flag 0x800)	`flag_counts_supplementary_pass`
\|\|	Duplicate	Number of reads marked as duplicates, including both primary and nonprimary alignments (SAM flag 0x400)	`flag_counts_duplicates_pass`
\|\|	Primary Duplicate	Number of primary alignment reads marked as duplicates (SAM flag 0x400, excluding secondary/supplementary)	`flag_counts_primary_duplicates_pass`
\|\|	Mapped	Number of reads that aligned to the reference, including secondary and supplementary alignments	`flag_counts_mapped_pass`
\|\|	Primary Mapped	Number of primary alignment reads: the best alignment for each read segment	`flag_counts_primary_mapped_pass`
\|\|	Paired	Number of reads originating from paired end sequencing (SAM flag 0x1)	`flag_counts_paired_in_sequencing_pass`
\|\|	Read 1	Number of reads identified as the first read in a pair (SAM flag 0x40)	`flag_counts_read1_pass`
\|\|	Read 2	Number of reads identified as the second read in a pair (SAM flag 0x80)	`flag_counts_read2_pass`
\|\|	Properly Paired	Number of reads mapped in a proper pair: correct orientation, expected insert size, same chromosome (SAM flag 0x2)	`flag_counts_properly_paired_pass`
\|\|	Properly Paired Mate Mapped	Number of properly paired reads where both the read and its mate are mapped (flags 0x1 + 0x2, excluding flag 0x8)	`flag_counts_properly_paired_mate_mapped_pass`
\|\|	Singleton	Number of paired reads that are mapped but whose mate is unmapped (orphaned read ends)	`flag_counts_singletons_pass`
\|\|	Mate Diff Chrm	Number of reads where both ends are mapped but to different chromosomes; indicates structural variants	`flag_counts_mate_diff_chrm_pass`
\|\|	Mate Diff Chrm MAPQ≥5	Number of mate pairs on different chromosomes with mapping quality ≥5; high confidence interchromosomal rearrangements	`flag_counts_mate_diff_chrm_mapq_5_pass`

Coverage

Created with MultiQC

Fragment Length

Created with MultiQC

PURPLE

https://github.com/hartwigmedical/hmftools/tree/master/purple

QC

Showing ¹/₁ rows and ¹²/₁₃ columns.

Sample Name	Status	AMBER Gender	COBALT Gender	Purity	Contamination	TINC	LOH	AMBER Mean Depth	Germline Aberrations	Method	Deleted Genes	Copy Number Segments	Unsupported Copy Number Segments
HCC1395 HCC1395.tumor_dna	Pass	Male	Male	100.00%	0.00%	0.00%	52.43%	89	NONE	Normal	148	2755	1

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: table-5975237_table

Sort	Column	Description	ID
\|\|	Status	Overall PURPLE QC status: PASS or FAIL based on quality metrics and solution reliability	`qc_status`
\|\|	AMBER Gender	Patient sex prediction from AMBER B allele frequency data on sex chromosomes	`qc_amber_gender`
\|\|	COBALT Gender	Patient sex prediction from COBALT read depth ratio data on sex chromosomes	`qc_cobalt_gender`
\|\|	Purity	Tumor purity estimate from the QC file: the proportion of tumor derived cells in the sample	`qc_purity`
\|\|	Contamination	Estimated cross sample contamination percentage: abnormal allele frequencies from contaminating DNA	`qc_contamination`
\|\|	TINC	Tumor in normal contamination: estimated percentage of tumor DNA detected in the matched normal reference sample	`qc_tinc`
\|\|	LOH	Percentage of the genome showing loss of heterozygosity: genomic regions where one allele has been lost	`qc_loh`
\|\|	AMBER Mean Depth	Mean sequencing depth at AMBER BAF SNP sites, used to assess BAF signal reliability	`qc_amber_mean_depth`
\|\|	Germline Aberrations	Classification of detected germline copy number aberrations: NONE, MOSAIC, or REPORTED based on clinical significance	`qc_germline_aberrations`
\|\|	Method	Purity estimation method used: BAF based for paired tumor with normal analysis	`qc_method`
\|\|	Deleted Genes	Number of genes with deep (homozygous) deletions detected: complete loss of both gene copies	`qc_deleted_genes`
\|\|	Copy Number Segments	Number of discrete copy number segments identified in the tumor genome by the segmentation algorithm	`qc_copy_number_segments`
\|\|	Unsupported Copy Number Segments	Number of copy number segments lacking sufficient BAF or read depth evidence: elevated counts indicate poor fit quality or noisy data	`qc_unsupported_copy_number_segments`

Purity Summary

Showing ¹/₁ rows and ¹⁴/₁₈ columns.

Sample Name	Status	Purity	Ploidy	Score	Whole Genome Duplication	Gender	Normalisation Factor	Diploid Proportion	Polyclonal Proportion	Purity Minimum	Purity Maximum	Ploidy Minimum	Ploidy Maximum	Diploid Proportion Minimum	Diploid Proportion Maximum	Somatic Penalty	Run Mode	Targeted
HCC1395 HCC1395.tumor_dna	Normal	100.00%	2.8200	1.1930	True	Male	0.7100	1.77%	31.29%	98.00%	100.00%	1.3800	2.9400	1.70%	10.15%	0.0000	TUMOR_GERMLINE	False

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: table-6748050_table

Sort	Column	Description	ID
\|\|	Status	Overall PURPLE fit status: indicates whether a valid purity/ploidy solution was found	`purity_status`
\|\|	Purity	Estimated tumor cell fraction: the proportion of cells in the sample that are tumor derived	`purity_purity`
\|\|	Ploidy	Average copy number of the tumor genome (diploid = 2; tetraploid of ~4)	`purity_ploidy`
\|\|	Score	Deviation score of the purity/ploidy fit: lower is a better fit to the observed BAF and coverage data	`purity_score`
\|\|	Whole Genome Duplication	Whether the tumor has undergone whole genome duplication: ploidy ≥3 with widespread copy number changes	`purity_whole_genome_duplication`
\|\|	Gender	Predicted sex of the patient based on somatic copy number profile of sex chromosomes	`purity_gender`
\|\|	Normalisation Factor	Normalization factor applied to correct for tumor/normal sequencing depth differences	`purity_norm_factor`
\|\|	Diploid Proportion	Proportion of the genome estimated to be diploid, reflecting the normal copy number fraction	`purity_diploid_proportion`
\|\|	Polyclonal Proportion	Proportion of the genome exhibiting polyclonal copy number behavior, suggesting multiple subclonal populations	`purity_polyclonal_proportion`
\|\|	Purity Minimum	Lower bound of the confidence range for the estimated tumor purity	`purity_min_purity`
\|\|	Purity Maximum	Upper bound of the confidence range for the estimated tumor purity	`purity_max_purity`
\|\|	Ploidy Minimum	Lower bound of the confidence range for the estimated tumor ploidy	`purity_min_ploidy`
\|\|	Ploidy Maximum	Upper bound of the confidence range for the estimated tumor ploidy	`purity_max_ploidy`
\|\|	Diploid Proportion Minimum	Lower bound of the confidence range for the diploid genome proportion	`purity_min_diploid_proportion`
\|\|	Diploid Proportion Maximum	Upper bound of the confidence range for the diploid genome proportion	`purity_max_diploid_proportion`
\|\|	Somatic Penalty	Penalty applied to the fit score for deviations from expected somatic variant copy number patterns	`purity_somatic_penalty`
\|\|	Run Mode	PURPLE analysis mode: TUMOR NORMAL (paired) or TUMOR ONLY (unmatched)	`purity_run_mode`
\|\|	Targeted	Whether the sequencing was targeted (panel or exome): TMB and TML values are corrected for panel size if True	`purity_targeted`

Mutation Biomarkers

Showing ¹/₁ rows and ⁷/₇ columns.

Sample Name	MS Status	TML Status	TMB Status	MS INDELs per MB	TML	TMB per MB	SV TMB
HCC1395 HCC1395.tumor_dna	MSS	High	High	0.0965	349	14.8398	1295

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: table-2151968_table

Sort	Column	Description	ID
\|\|	MS Status	Microsatellite stability classification: MSS (stable), MSI-L (low instability), or MSI-H (high instability, dMMR)	`purity_ms_status`
\|\|	TML Status	TML clinical classification: HIGH or LOW relative to cohort threshold	`purity_tml_status`
\|\|	TMB Status	TMB clinical classification: HIGH (>10 muts/Mb) or LOW; high TMB predicts immunotherapy benefit	`purity_tmb_status`
\|\|	MS INDELs per MB	Microsatellite instability: number of small insertion and deletion events in microsatellite repeats per megabase	`purity_ms_indels_per_mb`
\|\|	TML	Tumor Mutational Load: number of missense somatic mutations per megabase of coding genome	`purity_tml`
\|\|	TMB per MB	Tumor Mutational Burden: all somatic coding variants (SNVs and indels) per megabase; biomarker for immunotherapy response	`purity_tmb_per_mb`
\|\|	SV TMB	Structural Variant Tumor Mutational Burden: number of somatic structural variants such as translocations and inversions	`purity_sv_tumor_mutational_burden`

Software Versions

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

Group	Software	Version
AMBER	amber	`4.3`
	bioconductor-copynumber	`1.38.0`
	java	`21-internal`
	r	`4.4.3`
BWAMEM2_ALIGN	bwa-mem2	`2.3`
	sambamba	`1.0.1`
	samtools	`1.21`
BamTools	bamtools	`1.6.1`
	java	`21-internal`
CHORD	chord	`2.1.2`
	java	`21-internal`
	r	`4.4.3`
	r-randomforest	`4.7.1.2`
CIDER	cider	`1.2`
	java	`21-internal`
COBALT	bioconductor-copynumber	`1.38.0`
	cobalt	`3.0`
	java	`21-internal`
	r	`4.4.3`
	r-dplyr	`1.2.1`
CUPPA	cuppa	`2.5.1`
	java	`21-internal`
	numpy	`1.26.4`
	pandas	`2.0.3`
	python	`3.11.15`
	r	`4.2.3`
	r-ggplot2	`3.5.1`
	scikit-learn	`1.3.0`
ESVEE	esvee	`2.0.1`
	java	`22.0.1-internal`
	sambamba	`1.0.1`
GATK4_MARKDUPLICATES	gatk4	`4.6.1.0`
ISOFOX	isofox	`2.0.1`
	java	`21-internal`
LILAC	java	`21-internal`
	lilac	`2.0`
LINXREPORT	linxreport	`1.2.0`
	r	`4.5.3`
	r-dplyr	`1.2.1`
LINX_GERMLINE	java	`21-internal`
	linx	`2.3.1`
LINX_SOMATIC	java	`21-internal`
	linx	`2.3.1`
LINX_VISUALISER	circos	`0.69-8`
	java	`21-internal`
	linx	`2.3.1`
	r	`4.5.3`
	r-dplyr	`1.2.1`
	r-ggplot2	`4.0.3`
NEO_ANNOTATE_FUSIONS	isofox	`2.0.1`
	java	`21-internal`
NEO_FINDER	java	`21-internal`
	neo	`1.3`
NEO_SCORER	java	`21-internal`
	neo	`1.3`
ORANGE	java	`21-internal`
	orange	`5.0.1`
PAVE_GERMLINE	java	`21-internal`
	pave	`1.9`
PAVE_SOMATIC	java	`21-internal`
	pave	`1.9`
PEACH	java	`21-internal`
	peach	`2.0.0`
PURPLE	circos	`0.69-8`
	java	`21-internal`
	purple	`4.4`
	r	`4.5.3`
	r-dplyr	`1.2.1`
	r-ggplot2	`4.0.3`
QSEE	qsee	`1.0`
	r	`4.5.3`
	r-dplyr	`1.2.1`
	r-ggplot2	`4.0.3`
REDUX	java	`21-internal`
	r	`4.5.3`
	r-dplyr	`1.2.1`
	r-ggplot2	`4.0.3`
	redux	`2.0.5`
	samtools	`1.24`
SAGE_APPEND_GERMLINE	java	`21-internal`
	sage	`5.0.2`
SAGE_APPEND_SOMATIC	java	`21-internal`
	sage	`5.0.2`
SAGE_GERMLINE	java	`21-internal`
	sage	`5.0.2`
SAGE_SOMATIC	java	`21-internal`
	sage	`5.0.2`
SAGE_VISUALISER	java	`21-internal`
	sage	`5.0.2`
SAMTOOLS_SORT	samtools	`1.21`
SIGS	java	`21-internal`
	sigs	`1.2.1`
STAR_ALIGN	star	`2.7.3a`
TEAL_PIPELINE	java	`21-internal`
	samtools	`1.23.1`
	teal	`1.4`
TEAL_PREP	java	`21-internal`
	samtools	`1.23.1`
	teal	`1.4`
VIRUSBREAKEND	bcftools	`1.19`
	bwa	`0.7.17-r1188`
	gridss	`2.13.2`
	java	`20.0.2-internal`
	kraken2	`2.1.3`
	r	`4.3.1`
	r-structuralvariantannotation	`1.18.0`
	repeatmasker	`4.1.5`
	samtools	`1.19.2`
VIRUSINTERPRETER	java	`21-internal`
	virusinterpreter	`1.7.2`
Workflow	Nextflow	`26.04.6`
	nf-core/oncoanalyser	`v3.0.0-g7c74c87`

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