MultiQC Report

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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 1.34

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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 Seqera.

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

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Report generated on 2026-04-30, 14:00 AEST based on data in: /Users/stephen/projects/oncoanalyser_multiqc_plugin/test_data/outputs

General Statistics

Showing ⁴/₄ rows and ¹¹/₁₁ columns.

Sample Name	Aligments	Reads	Mapped Reads	Properly Paired Reads	Duplicate Reads	Contamination	Ploidy	Purity	QC PURPLE	QC AMBER	Gender
case-colo829 hartwig-colo829.normal	720308024	702784421	99.61%	98.83%	10.65%
case-colo829 hartwig-colo829.tumor	2609124943	2551026318	99.60%	98.76%	14.62%	0.00%	3.1000	99.00%	Pass	Pass	Male
case-hcc1395 seqcii-hcc1395.normal	889908557	871408807	99.65%	98.68%	2.04%
case-hcc1395 seqcii-hcc1395.tumor	1808024698	1765297342	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	Aligments	Total number of alignments included QC-failed	`bamtools-flag_counts_alignments_total`
\|\|	BamTools	Reads	Total number of reads	`bamtools-flag_counts_reads_total`
\|\|	BamTools	Mapped Reads	Percentage of mapped reads	`bamtools-flag_counts_reads_mapped_pct`
\|\|	BamTools	Properly Paired Reads	Properly paired reads	`bamtools-flag_counts_reads_pp_pct`
\|\|	BamTools	Duplicate Reads	Percentage of duplicate reads	`bamtools-flag_counts_reads_dup_pct`
\|\|	AMBER	Contamination	Percentage of contamination	`amber-qc_contamination`
\|\|	PURPLE	Ploidy	Ploidy	`purple-purity_ploidy`
\|\|	PURPLE	Purity	Percentage purity	`purple-purity_purity`
\|\|	PURPLE	QC PURPLE	Status	`purple-qc_status`
\|\|	AMBER	QC AMBER	QC status	`amber-qc_status`
\|\|	PURPLE	Gender	Gender	`purple-purity_gender`

AMBER

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

Showing ⁴/₄ rows and ⁵/₇ columns.

Sample Name	Status	Consanguinity Proportion	Contamination	Contamination Sites	Homozygous Regions Pass	Homozygous Regions Total	Uniparental Disomy
case-colo829 hartwig-colo829.normal					0	252
case-colo829 hartwig-colo829.tumor	Pass	0.00%	0.00%	23425			NONE
case-hcc1395 seqcii-hcc1395.normal					3	253
case-hcc1395 seqcii-hcc1395.tumor	Pass	2.61%	0.00%	55643			NONE

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: table-7238713_table

Sort	Column	Description	ID
\|\|	Status	QC status	`qc_status`
\|\|	Consanguinity Proportion	Proportion of consanguinity	`qc_consanguinity_proportion`
\|\|	Contamination	Percentage of contamination	`qc_contamination`
\|\|	Contamination Sites	Number of sites assessed for contamination	`contamination_sites_count`
\|\|	Homozygous Regions Pass	Number of passing homozygous regions	`homozygousregions_pass`
\|\|	Homozygous Regions Total	Total number of homozygous regions	`homozygousregions_total`
\|\|	Uniparental Disomy	Uniparental Disomy	`qc_uniparental_disomy`

BamTools

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

Summary

Showing ⁴/₄ rows and ²⁸/₂₈ columns.

Sample Name	Total Region Bases	Total Reads	Duplicate 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
case-colo829 hartwig-colo829.normal	2924985581	703608192	74883451	30.65	9.64	32.00	5.00	3.36%	10.50%	0.28%	0.01%	0.49%	0.00%	97.78%	97.17%	96.43%	94.09%	90.11%	81.68%	61.41%	13.08%	0.98%	0.18%	0.10%	0.07%	0.05%	0.03%
case-colo829 hartwig-colo829.tumor	2924985581	2554019777	373222555	105.71	36.86	108.00	24.00	3.25%	14.40%	0.29%	0.01%	0.73%	0.16%	97.36%	96.93%	96.72%	96.57%	96.45%	96.33%	96.20%	95.92%	95.43%	93.21%	85.95%	76.37%	69.35%	60.96%
case-hcc1395 seqcii-hcc1395.normal	2924985581	873388001	17745000	40.93	14.22	43.00	8.00	3.59%	1.97%	0.24%	0.30%	1.03%	0.01%	97.21%	96.62%	96.15%	95.07%	92.33%	87.79%	82.19%	61.85%	26.80%	5.06%	0.57%	0.18%	0.13%	0.09%
case-hcc1395 seqcii-hcc1395.tumor	2924985581	1769411736	65159274	80.61	39.60	75.00	22.00	3.94%	3.56%	0.26%	0.28%	1.53%	0.10%	96.75%	96.17%	95.91%	95.66%	95.25%	94.47%	93.13%	89.21%	83.00%	71.19%	56.42%	44.54%	35.28%	27.18%

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: table-3688208_table

Sort	Column	Description	ID
\|\|	Total Region Bases	Total region bases	`summary_total_region_bases`
\|\|	Total Reads	Total reads (pass only)	`summary_total_reads`
\|\|	Duplicate Reads	Duplicate reads	`summary_duplicate_reads`
\|\|	Dual Strand Reads	Dual strand reads	`summary_dual_strand_reads`
\|\|	Mean Coverage	Mean coverage	`summary_mean_coverage`
\|\|	Std Dev Coverage	Std dev coverage	`summary_std_dev_coverage`
\|\|	Median Coverage	Median coverage	`summary_median_coverage`
\|\|	MAD Coverage	MAD coverage	`summary_mad_coverage`
\|\|	Low Map Qual	Low map qual	`summary_low_map_qual_percent`
\|\|	Duplicate	Duplicate	`summary_duplicate_percent`
\|\|	Unmapped	Unmapped	`summary_unmapped_percent`
\|\|	Low Base Qual	Low base qual	`summary_low_base_qual_percent`
\|\|	Overlapping Read	Overlapping read	`summary_overlapping_read_percent`
\|\|	Capped Coverage	Capped coverage	`summary_capped_coverage`
\|\|	Depth Coverage 1	Depth coverage 1	`summary_depth_coverage_1`
\|\|	Depth Coverage 5	Depth coverage 5	`summary_depth_coverage_5`
\|\|	Depth Coverage 10	Depth coverage 10	`summary_depth_coverage_10`
\|\|	Depth Coverage 15	Depth coverage 15	`summary_depth_coverage_15`
\|\|	Depth Coverage 20	Depth coverage 20	`summary_depth_coverage_20`
\|\|	Depth Coverage 25	Depth coverage 25	`summary_depth_coverage_25`
\|\|	Depth Coverage 30	Depth coverage 30	`summary_depth_coverage_30`
\|\|	Depth Coverage 40	Depth coverage 40	`summary_depth_coverage_40`
\|\|	Depth Coverage 50	Depth coverage 50	`summary_depth_coverage_50`
\|\|	Depth Coverage 60	Depth coverage 60	`summary_depth_coverage_60`
\|\|	Depth Coverage 70	Depth coverage 70	`summary_depth_coverage_70`
\|\|	Depth Coverage 80	Depth coverage 80	`summary_depth_coverage_80`
\|\|	Depth Coverage 90	Depth coverage 90	`summary_depth_coverage_90`
\|\|	Depth Coverage 100	Depth coverage 100	`summary_depth_coverage_100`

Flag Statistics

Showing ⁴/₄ rows and ¹⁹/₁₉ columns.

Sample Name	Aligments	Reads	Mapped Reads	Duplicate Reads	Properly Paired Reads	Supplementary	Duplicate	Primary Duplicate	Mapped	Primary Mapped	Paired	Read 1	Read 2	Properly Paired	Properly Properly Mate Mapped	Singleton	Mate Diff Chrm	Mate Diff Chrm MAPQ>=5
case-colo829 hartwig-colo829.normal	720308024	702784421	99.61%	10.65%	98.83%	823771	74883451	74857435	700878318	700054547	702784421	351394086	351390335	694537578	697324673	2729874	1954639	1219564
case-colo829 hartwig-colo829.tumor	2609124943	2551026318	99.60%	14.62%	98.76%	2993459	373222555	373078494	2543818329	2540824870	2551026318	1275521122	1275505196	2519470036	2530623422	10201448	7989738	5135948
case-hcc1395 seqcii-hcc1395.normal	889908557	871408807	99.65%	2.04%	98.68%	1979194	17745000	17739145	870377423	868398229	871408807	435691086	435717721	859916638	865387651	3010578	2525957	1510216
case-hcc1395 seqcii-hcc1395.tumor	1808024698	1765297342	99.63%	3.69%	98.72%	4114394	65159274	65137183	1762895754	1758781360	1765297342	882625967	882671375	1742667324	1752265378	6515982	4700156	2698508

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: table-7044271_table

Sort	Column	Description	ID
\|\|	Aligments	Total number of alignments included QC-failed	`flag_counts_alignments_total`
\|\|	Reads	Total number of reads	`flag_counts_reads_total`
\|\|	Mapped Reads	Percentage of mapped reads	`flag_counts_reads_mapped_pct`
\|\|	Duplicate Reads	Percentage of duplicate reads	`flag_counts_reads_dup_pct`
\|\|	Properly Paired Reads	Properly paired reads	`flag_counts_reads_pp_pct`
\|\|	Secondary	Secondary	`flag_counts_secondary_pass`
\|\|	Supplementary	Supplementary	`flag_counts_supplementary_pass`
\|\|	Duplicate	Duplicate	`flag_counts_duplicates_pass`
\|\|	Primary Duplicate	Primary duplicate	`flag_counts_primary_duplicates_pass`
\|\|	Mapped	Mapped	`flag_counts_mapped_pass`
\|\|	Primary Mapped	Primary mapped	`flag_counts_primary_mapped_pass`
\|\|	Paired	Paired	`flag_counts_paired_in_sequencing_pass`
\|\|	Read 1	Read 1	`flag_counts_read1_pass`
\|\|	Read 2	Read 2	`flag_counts_read2_pass`
\|\|	Properly Paired	Properly paired	`flag_counts_properly_paired_pass`
\|\|	Properly Properly Mate Mapped	Properly properly mate mapped	`flag_counts_properly_paired_mate_mapped_pass`
\|\|	Singleton	Singleton	`flag_counts_singletons_pass`
\|\|	Mate Diff Chrm	Mate diff chrm	`flag_counts_mate_diff_chrm_pass`
\|\|	Mate Diff Chrm MAPQ>=5	Mate diff chrm MAPQ>=5	`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 ²/₂ 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
case-colo829 hartwig-colo829.tumor	Pass	Male	Male	99.00%	0.00%	0.00%	19.25%	108	NONE	Normal	4	238	0
case-hcc1395 seqcii-hcc1395.tumor	Pass	Male	Male	100.00%	0.00%	0.00%	52.43%	76	NONE	Normal	147	2741	4

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: table-2760105_table

Sort	Column	Description	ID
\|\|	Status	Status	`qc_status`
\|\|	AMBER Gender	AMBER gender	`qc_amber_gender`
\|\|	COBALT Gender	COBALT gender	`qc_cobalt_gender`
\|\|	Purity	Purity	`qc_purity`
\|\|	Contamination	Contamination	`qc_contamination`
\|\|	TINC	TINC	`qc_tinc`
\|\|	LOH	LOH	`qc_loh`
\|\|	AMBER Mean Depth	AMBER mean depth	`qc_amber_mean_depth`
\|\|	Germline Aberrations	Germline aberrations	`qc_germline_aberrations`
\|\|	Method	Method	`qc_method`
\|\|	Deleted Genes	Deleted genes	`qc_deleted_genes`
\|\|	Copy Number Segments	Copy number segements	`qc_copy_number_segments`
\|\|	Unsupported Copy Number Segments	Unsupported copy number segements	`qc_unsupported_copy_number_segments`

Purity Summary

Showing ²/₂ 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
case-colo829 hartwig-colo829.tumor	Normal	99.00%	3.1000	0.6159	True	Male	0.6457	2.12%	9.16%	97.00%	100.00%	3.0500	3.1500	2.12%	2.12%	0.0000	TUMOR_GERMLINE	False
case-hcc1395 seqcii-hcc1395.tumor	Normal	100.00%	2.8200	1.1965	True	Male	0.7084	1.74%	30.82%	98.00%	100.00%	1.3800	2.9400	1.67%	9.85%	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-7093546_table

Sort	Column	Description	ID
\|\|	Status	Status	`purity_status`
\|\|	Purity	Percentage purity	`purity_purity`
\|\|	Ploidy	Ploidy	`purity_ploidy`
\|\|	Score	Score	`purity_score`
\|\|	Whole Genome Duplication	Whole genome duplication	`purity_whole_genome_duplication`
\|\|	Gender	Gender	`purity_gender`
\|\|	Normalisation factor	Normalisation factor	`purity_norm_factor`
\|\|	Diploid Proportion	Percentage diploid proportion	`purity_diploid_proportion`
\|\|	Polyclonal proportion	Polyclonal proportion	`purity_polyclonal_proportion`
\|\|	Purity Minimum	Minimum purity	`purity_min_purity`
\|\|	Purity Maximum	Maximum purity	`purity_max_purity`
\|\|	Ploidy Minimum	Minimum ploidy	`purity_min_ploidy`
\|\|	Ploidy Maximum	Maximum ploidy	`purity_max_ploidy`
\|\|	Diploid Proportion Minimum	Minimum diploid proportion	`purity_min_diploid_proportion`
\|\|	Diploid Proportion Maximum	Maximum diploid proportion	`purity_max_diploid_proportion`
\|\|	Somatic Penalty	Somatic penalty	`purity_somatic_penalty`
\|\|	Run Mode	Run mode	`purity_run_mode`
\|\|	Targeted	Targeted	`purity_targeted`

Mutational Load

Showing ²/₂ rows and ⁷/₇ columns.

Sample Name	MS Status	TML Status	TMB Status	MS INDELs per MB	TML	TMB per MB	SV TMB
case-colo829 hartwig-colo829.tumor	MSS	High	High	0.0745	187	13.7391	93
case-hcc1395 seqcii-hcc1395.tumor	MSS	High	High	0.1035	350	14.9171	1275

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: table-4324852_table

Sort	Column	Description	ID
\|\|	MS Status	MS status	`purity_ms_status`
\|\|	TML Status	TML status	`purity_tml_status`
\|\|	TMB Status	TMB status	`purity_tmb_status`
\|\|	MS INDELs per MB	MS INDELs per MB	`purity_ms_indels_per_mb`
\|\|	TML	TML	`purity_tml`
\|\|	TMB per MB	TMB per MB	`purity_tmb_per_mb`
\|\|	SV TMB	SV TMB	`purity_sv_tumor_mutational_burden`

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