REGRESSION

MultiQC Report for DAQ. Includes data from all the QC tools in DAQ.

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Report generated on 2026-06-01, 21:51 UTC based on data in: /tmp/nxf.NDoo6Jis0C

General Statistics

Showing ³⁶/₃₆ rows and ¹⁸/₃₃ columns.

Sample Name	≥ 1X	≥ 5X	≥ 10X	≥ 30X	≥ 50X	Median	Mean Cov.	Min Cov.	Max Cov.	Mb Total Coverage Bases	Genome length	Fold Enrichment	Target Bases ≥ 30X	Insert Size	Mean Insert Size	Duplication	Error rate	Non-primary	Reads mapped	% Mapped	% Proper pairs	% MapQ 0 reads	Total seqs	Mean insert	% Duplication	% > Q30	Mb Q30 bases	Reads After Filtering	GC content	% PF	% Adapter	Mean R1 Length	Mean R2 Length
HCC1395_BL	1.0%	1.0%	1.0%	1.0%	1.0%	0X	1.4X	0.0X	840.0X	51.1Mb	37919873	39X	1%	275bp	302bp	14.7%	0.43%	0.0M	1.0M	100.0%	99.9%	12.9%	1.0M	304.8bp
HCC1395_BL_S2_L001																									0.9%	94.6%	17.1Mb	0.1M	50.6%	100.0%	15.3%	150.0bp	150.0bp
HCC1395_BL_S2_L002																									0.9%	94.6%	17.0Mb	0.1M	50.4%	100.0%	15.5%	150.0bp	150.0bp
HCC1395_BL_S2_L003																									0.9%	94.5%	17.0Mb	0.1M	50.5%	100.0%	15.3%	150.0bp	150.0bp
HCC1395_BL_S2_L004																									0.9%	94.6%	17.1Mb	0.1M	50.5%	100.0%	15.4%	150.0bp	150.0bp
HCC1395_BL_S2_L005																									0.9%	94.5%	17.1Mb	0.1M	50.5%	100.0%	15.3%	150.0bp	150.0bp
HCC1395_BL_S2_L006																									0.9%	94.6%	17.0Mb	0.1M	50.4%	100.0%	15.5%	150.0bp	150.0bp
HCC1395_BL_S2_L007																									0.9%	94.6%	17.1Mb	0.1M	50.5%	100.0%	15.5%	150.0bp	150.0bp
HCC1395_BL_S2_L008																									0.9%	94.5%	17.1Mb	0.1M	50.5%	100.0%	15.4%	150.0bp	150.0bp
HCC1395_tumor	1.0%	1.0%	1.0%	1.0%	1.0%	0X	1.3X	0.0X	710.0X	48.1Mb	37919873	39X	1%	265bp	292bp	16.9%	0.49%	0.0M	1.0M	100.0%	99.9%	13.0%	1.0M	296.6bp
HCC1395_tumor_S1_L001																									1.1%	95.0%	17.0Mb	0.1M	50.3%	100.0%	16.3%	150.0bp	150.0bp
HCC1395_tumor_S1_L002																									1.1%	94.9%	17.2Mb	0.1M	50.2%	100.0%	16.2%	150.0bp	150.0bp
HCC1395_tumor_S1_L003																									1.2%	94.9%	17.0Mb	0.1M	50.3%	100.0%	16.3%	150.0bp	150.0bp
HCC1395_tumor_S1_L004																									1.1%	95.0%	17.0Mb	0.1M	50.2%	100.0%	16.2%	150.0bp	150.0bp
HCC1395_tumor_S1_L005																									1.1%	95.0%	17.1Mb	0.1M	50.4%	100.0%	16.6%	150.0bp	150.0bp
HCC1395_tumor_S1_L006																									1.1%	95.0%	17.1Mb	0.1M	50.2%	100.0%	16.6%	150.0bp	150.0bp
HCC1395_tumor_S1_L007																									1.1%	95.0%	17.1Mb	0.1M	50.3%	100.0%	16.7%	150.0bp	150.0bp
HCC1395_tumor_S1_L008																									1.2%	95.0%	17.2Mb	0.1M	50.2%	100.0%	16.5%	150.0bp	150.0bp
Sig_18_Blood	1.0%	1.0%	1.0%	1.0%	1.0%	0X	1.4X	0.0X	909.0X	54.9Mb	37919873	40X	1%	280bp	307bp	11.6%	0.45%	0.0M	1.0M	100.0%	99.9%	12.3%	1.0M	312.7bp
Sig_18_Blood_S4_L001																									0.9%	94.5%	17.2Mb	0.1M	49.9%	100.0%	14.2%	150.0bp	150.0bp
Sig_18_Blood_S4_L002																									0.9%	94.6%	17.1Mb	0.1M	49.7%	100.0%	14.2%	150.0bp	150.0bp
Sig_18_Blood_S4_L003																									0.9%	94.6%	17.2Mb	0.1M	49.8%	100.0%	14.3%	150.0bp	150.0bp
Sig_18_Blood_S4_L004																									1.0%	94.6%	17.2Mb	0.1M	49.8%	100.0%	14.2%	150.0bp	150.0bp
Sig_18_Blood_S4_L005																									0.9%	94.6%	17.1Mb	0.1M	49.7%	100.0%	14.1%	150.0bp	150.0bp
Sig_18_Blood_S4_L006																									0.9%	94.5%	17.1Mb	0.1M	49.8%	100.0%	14.1%	150.0bp	150.0bp
Sig_18_Blood_S4_L007																									0.8%	94.6%	17.1Mb	0.1M	49.8%	100.0%	14.5%	150.0bp	150.0bp
Sig_18_Blood_S4_L008																									0.9%	94.6%	17.1Mb	0.1M	49.9%	100.0%	14.0%	150.0bp	150.0bp
Sig_18_tissue	1.0%	1.0%	1.0%	1.0%	1.0%	0X	1.4X	0.0X	937.0X	54.9Mb	37922265	43X	1%	218bp	242bp	8.4%	0.51%	0.0M	1.0M	100.0%	99.9%	11.9%	1.0M	244.5bp
Sig_18_tissue_S3_L001																									0.8%	95.9%	17.0Mb	0.1M	50.1%	100.0%	23.6%	150.0bp	150.0bp
Sig_18_tissue_S3_L002																									0.7%	95.9%	17.0Mb	0.1M	50.1%	100.0%	23.0%	150.0bp	150.0bp
Sig_18_tissue_S3_L003																									0.8%	95.9%	17.1Mb	0.1M	50.2%	100.0%	23.4%	150.0bp	150.0bp
Sig_18_tissue_S3_L004																									0.8%	95.8%	16.9Mb	0.1M	50.1%	100.0%	23.5%	150.0bp	150.0bp
Sig_18_tissue_S3_L005																									0.8%	95.9%	16.9Mb	0.1M	50.2%	100.0%	23.4%	150.0bp	150.0bp
Sig_18_tissue_S3_L006																									0.7%	95.9%	16.9Mb	0.1M	50.1%	100.0%	23.5%	150.0bp	150.0bp
Sig_18_tissue_S3_L007																									0.8%	95.9%	17.0Mb	0.1M	50.2%	100.0%	23.7%	150.0bp	150.0bp
Sig_18_tissue_S3_L008																									0.8%	95.9%	16.8Mb	0.1M	50.2%	100.0%	23.5%	150.0bp	150.0bp

Expand table

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	Scale
\|\|	Mosdepth	≥ 1X	Fraction of genome with at least 1X coverage	`mosdepth-1_x_pc`
\|\|	Mosdepth	≥ 5X	Fraction of genome with at least 5X coverage	`mosdepth-5_x_pc`
\|\|	Mosdepth	≥ 10X	Fraction of genome with at least 10X coverage	`mosdepth-10_x_pc`
\|\|	Mosdepth	≥ 30X	Fraction of genome with at least 30X coverage	`mosdepth-30_x_pc`
\|\|	Mosdepth	≥ 50X	Fraction of genome with at least 50X coverage	`mosdepth-50_x_pc`
\|\|	Mosdepth	Median	Median coverage	`mosdepth-median_coverage`
\|\|	Mosdepth	Mean Cov.	Mean coverage	`mosdepth-mean_coverage`
\|\|	Mosdepth	Min Cov.	Minimum coverage	`mosdepth-min_coverage`
\|\|	Mosdepth	Max Cov.	Maximum coverage	`mosdepth-max_coverage`
\|\|	Mosdepth	Mb Total Coverage Bases	Total coverage of bases (millions)	`mosdepth-coverage_bases`	base_count
\|\|	Mosdepth	Genome length	Total length of the genome	`mosdepth-length`
\|\|	Picard: HsMetrics	Fold Enrichment	Fold Enrichment	`picard_hsmetrics-FOLD_ENRICHMENT`
\|\|	Picard: HsMetrics	Target Bases ≥ 30X	Percent of target bases with coverage ≥ 30X	`picard_hsmetrics-picard_target_bases_30X`
\|\|	Picard: InsertSizeMetrics	Insert Size	Median Insert Size, all read orientations (bp)	`picard_insertsizemetrics-summed_median`
\|\|	Picard: InsertSizeMetrics	Mean Insert Size	Mean Insert Size, all read orientations (bp)	`picard_insertsizemetrics-summed_mean`
\|\|	Picard: Mark Duplicates	Duplication	Mark Duplicates - Percent Duplication	`picard_mark_duplicates-PERCENT_DUPLICATION`
\|\|	Samtools: stats	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`samtools_stats-error_rate`
\|\|	Samtools: stats	Non-primary	Non-primary alignments (millions)	`samtools_stats-non_primary_alignments`	read_count
\|\|	Samtools: stats	Reads mapped	Reads mapped in the bam file (millions)	`samtools_stats-reads_mapped`	read_count
\|\|	Samtools: stats	% Mapped	% Mapped reads	`samtools_stats-reads_mapped_percent`
\|\|	Samtools: stats	% Proper pairs	% Properly paired reads	`samtools_stats-reads_properly_paired_percent`
\|\|	Samtools: stats	% MapQ 0 reads	% of reads that are ambiguously placed (MapQ=0)	`samtools_stats-reads_MQ0_percent`
\|\|	Samtools: stats	Total seqs	Total sequences in the bam file (millions)	`samtools_stats-raw_total_sequences`	read_count
\|\|	Samtools: stats	Mean insert	Average insert size	`samtools_stats-insert_size_average`
\|\|	fastp	% Duplication	Duplication rate before filtering	`fastp-pct_duplication`
\|\|	fastp	% > Q30	Percentage of reads > Q30 after filtering	`fastp-after_filtering_q30_rate`
\|\|	fastp	Mb Q30 bases	Bases > Q30 after filtering (millions)	`fastp-after_filtering_q30_bases`	base_count
\|\|	fastp	Reads After Filtering	Total reads after filtering (millions)	`fastp-filtering_result_passed_filter_reads`	read_count
\|\|	fastp	GC content	GC content after filtering	`fastp-after_filtering_gc_content`
\|\|	fastp	% PF	Percent reads passing filter	`fastp-pct_surviving`
\|\|	fastp	% Adapter	Percentage adapter-trimmed reads	`fastp-pct_adapter`
\|\|	fastp	Mean R1 Length	Mean read length of R1	`fastp-before_filtering_read1_mean_length`
\|\|	fastp	Mean R2 Length	Mean read length of R2	`fastp-before_filtering_read2_mean_length`

Seqtool

Seqtool performs qc analyses on sequencing alignments.

Basic Stats

Full summary statistics from seqtool output.

Showing ⁴/₄ rows and ⁷⁰/₇₀ columns.

Sample Name	reads	unmapped	unique_reads	pairs	proper_pairs	pairs_on_target	pairs_off_target	reads_on_target	reads_off_target	dupes	frac_dupes	frac_reads_off_target	frac_pairs_off_target	frac_proper_pairs	frag_size_q20	frag_size_median	frag_size_q80	frag_size_mean	frag_size_std	n_q20	n_q25	n_q30	n_bases	mean_depth	cv_depth	max_depth	lt100x	lt700x	n_bases_gt30x	n_bases_gt100x	gc_0.35	gc_0.4	gc_0.45	gc_0.55	gc_0.6	gc_0.65	gc_0.7	bed	saturation_at_1000000_reads	roi_size	n_sites	loglik	lrt	bed_base_count
HCC1395_BL_full_basic_stats	999992.0	9.0	853439.0	426713.0	426416.0	4124.0	422292.0	6791.0	846639.0	146553.0	0.1	1.0	1.0	1.0	164.0	275.0	427.0	301.6	123.6	1.0	0.9	0.9	144359392.0	0.7	2.0	257.0	1.0	1.0	4843.0	1516.0	0.8	0.2	0.6	1.9	1.0	3.4	1.7	foresight_clarity_targets_hg38.bed	31.0	666239.0	76.0	-15.4	-0.0	667386.0
HCC1395_tumor_full_basic_stats	999980.0	4.0	830860.0	415427.0	414949.0	3614.0	411335.0	5971.0	824885.0	169120.0	0.2	1.0	1.0	1.0	159.0	265.0	414.0	291.9	119.9	1.0	0.9	0.9	143959508.0	0.6	2.0	241.0	1.0	1.0	4472.0	992.0	0.7	0.2	0.6	1.8	1.1	3.5	1.6	foresight_clarity_targets_hg38.bed	22.0	666239.0	76.0	-15.2	-0.0	667386.0
Sig_18_Blood_full_basic_stats	999982.0	7.0	884407.0	442197.0	441978.0	4003.0	437975.0	6498.0	877902.0	115575.0	0.1	1.0	1.0	1.0	168.0	280.0	436.0	307.4	125.7	1.0	0.9	0.9	144973902.0	0.7	2.0	266.0	1.0	1.0	4705.0	1182.0	0.8	0.2	0.6	2.0	1.0	3.3	1.4	foresight_clarity_targets_hg38.bed	27.0	666239.0	67.0	-11.3	-0.0	667386.0
Sig_18_tissue_full_basic_stats	999980.0	8.0	915604.0	457797.0	457316.0	3990.0	453326.0	7086.0	908510.0	84376.0	0.1	1.0	1.0	1.0	138.0	218.0	335.0	241.9	94.9	1.0	1.0	1.0	141505598.0	0.7	2.0	343.0	1.0	1.0	4511.0	1168.0	0.6	0.2	0.7	2.4	0.9	2.7	1.6	foresight_clarity_targets_hg38.bed	36.0	666239.0	66.0	-14.3	-0.0	667386.0

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

Sort	Column	Description	ID
\|\|	reads	reads	`seqtool-reads`
\|\|	unmapped	unmapped	`seqtool-unmapped`
\|\|	unique_reads	unique_reads	`seqtool-unique_reads`
\|\|	pairs	pairs	`seqtool-pairs`
\|\|	proper_pairs	proper_pairs	`seqtool-proper_pairs`
\|\|	pairs_on_target	pairs_on_target	`seqtool-pairs_on_target`
\|\|	pairs_off_target	pairs_off_target	`seqtool-pairs_off_target`
\|\|	reads_on_target	reads_on_target	`seqtool-reads_on_target`
\|\|	reads_off_target	reads_off_target	`seqtool-reads_off_target`
\|\|	dupes	dupes	`seqtool-dupes`
\|\|	frac_unmapped	frac_unmapped	`seqtool-frac_unmapped`
\|\|	frac_dupes	frac_dupes	`seqtool-frac_dupes`
\|\|	frac_reads_on_target	frac_reads_on_target	`seqtool-frac_reads_on_target`
\|\|	frac_reads_off_target	frac_reads_off_target	`seqtool-frac_reads_off_target`
\|\|	frac_pairs_on_target	frac_pairs_on_target	`seqtool-frac_pairs_on_target`
\|\|	frac_pairs_off_target	frac_pairs_off_target	`seqtool-frac_pairs_off_target`
\|\|	frac_proper_pairs	frac_proper_pairs	`seqtool-frac_proper_pairs`
\|\|	frac_bases_gt30x	frac_bases_gt30x	`seqtool-frac_bases_gt30x`
\|\|	frac_bases_gt100x	frac_bases_gt100x	`seqtool-frac_bases_gt100x`
\|\|	frag_size_q20	frag_size_q20	`seqtool-frag_size_q20`
\|\|	frag_size_median	frag_size_median	`seqtool-frag_size_median`
\|\|	frag_size_q80	frag_size_q80	`seqtool-frag_size_q80`
\|\|	frag_size_mean	frag_size_mean	`seqtool-frag_size_mean`
\|\|	frag_size_std	frag_size_std	`seqtool-frag_size_std`
\|\|	n_q20	n_q20	`seqtool-n_q20`
\|\|	n_q25	n_q25	`seqtool-n_q25`
\|\|	n_q30	n_q30	`seqtool-n_q30`
\|\|	n_bases	n_bases	`seqtool-n_bases`
\|\|	min_depth	min_depth	`seqtool-min_depth`
\|\|	mean_depth	mean_depth	`seqtool-mean_depth`
\|\|	cv_depth	cv_depth	`seqtool-cv_depth`
\|\|	max_depth	max_depth	`seqtool-max_depth`
\|\|	q1_depth	q1_depth	`seqtool-q1_depth`
\|\|	q5_depth	q5_depth	`seqtool-q5_depth`
\|\|	q50_depth	q50_depth	`seqtool-q50_depth`
\|\|	q95_depth	q95_depth	`seqtool-q95_depth`
\|\|	q99_depth	q99_depth	`seqtool-q99_depth`
\|\|	lt100x	lt100x	`seqtool-lt100x`
\|\|	lt700x	lt700x	`seqtool-lt700x`
\|\|	n_bases_gt30x	n_bases_gt30x	`seqtool-n_bases_gt30x`
\|\|	n_bases_gt100x	n_bases_gt100x	`seqtool-n_bases_gt100x`
\|\|	gc_0.0	gc_0.0	`seqtool-gc_0_0`
\|\|	gc_0.05	gc_0.05	`seqtool-gc_0_05`
\|\|	gc_0.1	gc_0.1	`seqtool-gc_0_1`
\|\|	gc_0.15	gc_0.15	`seqtool-gc_0_15`
\|\|	gc_0.2	gc_0.2	`seqtool-gc_0_2`
\|\|	gc_0.25	gc_0.25	`seqtool-gc_0_25`
\|\|	gc_0.3	gc_0.3	`seqtool-gc_0_3`
\|\|	gc_0.35	gc_0.35	`seqtool-gc_0_35`
\|\|	gc_0.4	gc_0.4	`seqtool-gc_0_4`
\|\|	gc_0.45	gc_0.45	`seqtool-gc_0_45`
\|\|	gc_0.5	gc_0.5	`seqtool-gc_0_5`
\|\|	gc_0.55	gc_0.55	`seqtool-gc_0_55`
\|\|	gc_0.6	gc_0.6	`seqtool-gc_0_6`
\|\|	gc_0.65	gc_0.65	`seqtool-gc_0_65`
\|\|	gc_0.7	gc_0.7	`seqtool-gc_0_7`
\|\|	gc_0.75	gc_0.75	`seqtool-gc_0_75`
\|\|	gc_0.8	gc_0.8	`seqtool-gc_0_8`
\|\|	gc_0.85	gc_0.85	`seqtool-gc_0_85`
\|\|	gc_0.9	gc_0.9	`seqtool-gc_0_9`
\|\|	gc_0.95	gc_0.95	`seqtool-gc_0_95`
\|\|	gc_1.0	gc_1.0	`seqtool-gc_1_0`
\|\|	bed	bed	`seqtool-bed`
\|\|	saturation_at_1000000_reads	saturation_at_1000000_reads	`seqtool-saturation_at_1000000_reads`
\|\|	roi_size	roi_size	`seqtool-roi_size`
\|\|	contam	contam	`seqtool-contam`
\|\|	n_sites	n_sites	`seqtool-n_sites`
\|\|	loglik	loglik	`seqtool-loglik`
\|\|	lrt	lrt	`seqtool-lrt`
\|\|	bed_base_count	bed_base_count	`seqtool-bed_base_count`

Depth Stats - all_targets

Depth and read QC statistics for all_targets panel.

Showing ⁴/₄ rows and ²⁶/₂₆ columns.

Sample Name	reads	unmapped	unique_reads	frac_dupes	pairs	frac_reads_on_target	frac_reads_off_target	frac_pairs_on_target	frac_pairs_off_target	frag_size_q20	frag_size_median	frag_size_q80	proper_pairs	frac_proper_pairs	pairs_on_target	pairs_off_target	reads_on_target	reads_off_target	frag_size_mean	frag_size_std	dupes	n_q20	n_q25	n_q30	n_bases
HCC1395_BL.md	999992.0	9.0	853439.0	0.1	426713.0	0.7	0.3	0.8	0.2	164.0	275.0	427.0	426416.0	1.0	329491.0	96925.0	573897.0	279533.0	301.6	123.6	146553.0	1.0	0.9	0.9	144359392.0
HCC1395_tumor.md	999980.0	4.0	830860.0	0.2	415427.0	0.7	0.3	0.8	0.2	159.0	265.0	414.0	414949.0	1.0	319733.0	95216.0	558413.0	272443.0	291.9	119.9	169120.0	1.0	0.9	0.9	143959508.0
Sig_18_Blood.md	999982.0	7.0	884407.0	0.1	442197.0	0.7	0.3	0.8	0.2	168.0	280.0	436.0	441978.0	1.0	346432.0	95546.0	602981.0	281419.0	307.4	125.7	115575.0	1.0	0.9	0.9	144973902.0
Sig_18_tissue.md	999980.0	8.0	915604.0	0.1	457797.0	0.7	0.3	0.8	0.2	138.0	218.0	335.0	457316.0	1.0	367376.0	89940.0	675835.0	239761.0	241.9	94.9	84376.0	1.0	1.0	1.0	141505598.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: seqtool_depth_stats_xgen_exome_hyb_panel_v2_targets_hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_bed_table

Sort	Column	Description	ID
\|\|	reads	reads	`seqtool-reads`
\|\|	unmapped	unmapped	`seqtool-unmapped`
\|\|	frac_unmapped	frac_unmapped	`seqtool-frac_unmapped`
\|\|	unique_reads	unique_reads	`seqtool-unique_reads`
\|\|	frac_dupes	frac_dupes	`seqtool-frac_dupes`
\|\|	pairs	pairs	`seqtool-pairs`
\|\|	frac_reads_on_target	frac_reads_on_target	`seqtool-frac_reads_on_target`
\|\|	frac_reads_off_target	frac_reads_off_target	`seqtool-frac_reads_off_target`
\|\|	frac_pairs_on_target	frac_pairs_on_target	`seqtool-frac_pairs_on_target`
\|\|	frac_pairs_off_target	frac_pairs_off_target	`seqtool-frac_pairs_off_target`
\|\|	frag_size_q20	frag_size_q20	`seqtool-frag_size_q20`
\|\|	frag_size_median	frag_size_median	`seqtool-frag_size_median`
\|\|	frag_size_q80	frag_size_q80	`seqtool-frag_size_q80`
\|\|	proper_pairs	proper_pairs	`seqtool-proper_pairs`
\|\|	frac_proper_pairs	frac_proper_pairs	`seqtool-frac_proper_pairs`
\|\|	pairs_on_target	pairs_on_target	`seqtool-pairs_on_target`
\|\|	pairs_off_target	pairs_off_target	`seqtool-pairs_off_target`
\|\|	reads_on_target	reads_on_target	`seqtool-reads_on_target`
\|\|	reads_off_target	reads_off_target	`seqtool-reads_off_target`
\|\|	frag_size_mean	frag_size_mean	`seqtool-frag_size_mean`
\|\|	frag_size_std	frag_size_std	`seqtool-frag_size_std`
\|\|	dupes	dupes	`seqtool-dupes`
\|\|	n_q20	n_q20	`seqtool-n_q20`
\|\|	n_q25	n_q25	`seqtool-n_q25`
\|\|	n_q30	n_q30	`seqtool-n_q30`
\|\|	n_bases	n_bases	`seqtool-n_bases`

Depth Stats - all_probes

Depth and read QC statistics for all_probes panel.

Showing ⁴/₄ rows and ²⁶/₂₆ columns.

Sample Name	reads	unmapped	unique_reads	frac_dupes	pairs	frac_reads_on_target	frac_reads_off_target	frac_pairs_on_target	frac_pairs_off_target	frag_size_q20	frag_size_median	frag_size_q80	proper_pairs	frac_proper_pairs	pairs_on_target	pairs_off_target	reads_on_target	reads_off_target	frag_size_mean	frag_size_std	dupes	n_q20	n_q25	n_q30	n_bases
HCC1395_BL.md	999992.0	9.0	853439.0	0.1	426713.0	0.7	0.3	0.8	0.2	164.0	275.0	427.0	426416.0	1.0	330561.0	95855.0	593587.0	259843.0	301.6	123.6	146553.0	1.0	0.9	0.9	144359392.0
HCC1395_tumor.md	999980.0	4.0	830860.0	0.2	415427.0	0.7	0.3	0.8	0.2	159.0	265.0	414.0	414949.0	1.0	320979.0	93970.0	578170.0	252686.0	291.9	119.9	169120.0	1.0	0.9	0.9	143959508.0
Sig_18_Blood.md	999982.0	7.0	884407.0	0.1	442197.0	0.7	0.3	0.8	0.2	168.0	280.0	436.0	441978.0	1.0	347479.0	94499.0	623225.0	261175.0	307.4	125.7	115575.0	1.0	0.9	0.9	144973902.0
Sig_18_tissue.md	999980.0	8.0	915604.0	0.1	457797.0	0.8	0.2	0.8	0.2	138.0	218.0	335.0	457316.0	1.0	368734.0	88582.0	693807.0	221789.0	241.9	94.9	84376.0	1.0	1.0	1.0	141505598.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: seqtool_depth_stats_xgen_exome_hyb_panel_v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint_bed_table

Sort	Column	Description	ID
\|\|	reads	reads	`seqtool-reads`
\|\|	unmapped	unmapped	`seqtool-unmapped`
\|\|	frac_unmapped	frac_unmapped	`seqtool-frac_unmapped`
\|\|	unique_reads	unique_reads	`seqtool-unique_reads`
\|\|	frac_dupes	frac_dupes	`seqtool-frac_dupes`
\|\|	pairs	pairs	`seqtool-pairs`
\|\|	frac_reads_on_target	frac_reads_on_target	`seqtool-frac_reads_on_target`
\|\|	frac_reads_off_target	frac_reads_off_target	`seqtool-frac_reads_off_target`
\|\|	frac_pairs_on_target	frac_pairs_on_target	`seqtool-frac_pairs_on_target`
\|\|	frac_pairs_off_target	frac_pairs_off_target	`seqtool-frac_pairs_off_target`
\|\|	frag_size_q20	frag_size_q20	`seqtool-frag_size_q20`
\|\|	frag_size_median	frag_size_median	`seqtool-frag_size_median`
\|\|	frag_size_q80	frag_size_q80	`seqtool-frag_size_q80`
\|\|	proper_pairs	proper_pairs	`seqtool-proper_pairs`
\|\|	frac_proper_pairs	frac_proper_pairs	`seqtool-frac_proper_pairs`
\|\|	pairs_on_target	pairs_on_target	`seqtool-pairs_on_target`
\|\|	pairs_off_target	pairs_off_target	`seqtool-pairs_off_target`
\|\|	reads_on_target	reads_on_target	`seqtool-reads_on_target`
\|\|	reads_off_target	reads_off_target	`seqtool-reads_off_target`
\|\|	frag_size_mean	frag_size_mean	`seqtool-frag_size_mean`
\|\|	frag_size_std	frag_size_std	`seqtool-frag_size_std`
\|\|	dupes	dupes	`seqtool-dupes`
\|\|	n_q20	n_q20	`seqtool-n_q20`
\|\|	n_q25	n_q25	`seqtool-n_q25`
\|\|	n_q30	n_q30	`seqtool-n_q30`
\|\|	n_bases	n_bases	`seqtool-n_bases`

Depth Stats - boosted_depth

Depth and read QC statistics for boosted_depth panel.

Showing ⁴/₄ rows and ²⁶/₂₆ columns.

Sample Name	reads	unmapped	unique_reads	frac_dupes	pairs	frac_reads_on_target	frac_reads_off_target	frac_pairs_on_target	frac_pairs_off_target	frag_size_q20	frag_size_median	frag_size_q80	proper_pairs	frac_proper_pairs	pairs_on_target	pairs_off_target	reads_on_target	reads_off_target	frag_size_mean	frag_size_std	dupes	n_q20	n_q25	n_q30	n_bases
HCC1395_BL.md	999992.0	9.0	853439.0	0.1	426713.0	0.4	0.6	0.5	0.5	164.0	275.0	427.0	426416.0	1.0	221377.0	205039.0	362511.0	490919.0	301.6	123.6	146553.0	1.0	0.9	0.9	144359392.0
HCC1395_tumor.md	999980.0	4.0	830860.0	0.2	415427.0	0.4	0.6	0.5	0.5	159.0	265.0	414.0	414949.0	1.0	223687.0	191262.0	370247.0	460609.0	291.9	119.9	169120.0	1.0	0.9	0.9	143959508.0
Sig_18_Blood.md	999982.0	7.0	884407.0	0.1	442197.0	0.4	0.6	0.5	0.5	168.0	280.0	436.0	441978.0	1.0	225144.0	216834.0	365965.0	518435.0	307.4	125.7	115575.0	1.0	0.9	0.9	144973902.0
Sig_18_tissue.md	999980.0	8.0	915604.0	0.1	457797.0	0.5	0.5	0.5	0.5	138.0	218.0	335.0	457316.0	1.0	242046.0	215270.0	428259.0	487337.0	241.9	94.9	84376.0	1.0	1.0	1.0	141505598.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: seqtool_depth_stats_altera_v3_targets_postQC_hg38_bed_table

Sort	Column	Description	ID
\|\|	reads	reads	`seqtool-reads`
\|\|	unmapped	unmapped	`seqtool-unmapped`
\|\|	frac_unmapped	frac_unmapped	`seqtool-frac_unmapped`
\|\|	unique_reads	unique_reads	`seqtool-unique_reads`
\|\|	frac_dupes	frac_dupes	`seqtool-frac_dupes`
\|\|	pairs	pairs	`seqtool-pairs`
\|\|	frac_reads_on_target	frac_reads_on_target	`seqtool-frac_reads_on_target`
\|\|	frac_reads_off_target	frac_reads_off_target	`seqtool-frac_reads_off_target`
\|\|	frac_pairs_on_target	frac_pairs_on_target	`seqtool-frac_pairs_on_target`
\|\|	frac_pairs_off_target	frac_pairs_off_target	`seqtool-frac_pairs_off_target`
\|\|	frag_size_q20	frag_size_q20	`seqtool-frag_size_q20`
\|\|	frag_size_median	frag_size_median	`seqtool-frag_size_median`
\|\|	frag_size_q80	frag_size_q80	`seqtool-frag_size_q80`
\|\|	proper_pairs	proper_pairs	`seqtool-proper_pairs`
\|\|	frac_proper_pairs	frac_proper_pairs	`seqtool-frac_proper_pairs`
\|\|	pairs_on_target	pairs_on_target	`seqtool-pairs_on_target`
\|\|	pairs_off_target	pairs_off_target	`seqtool-pairs_off_target`
\|\|	reads_on_target	reads_on_target	`seqtool-reads_on_target`
\|\|	reads_off_target	reads_off_target	`seqtool-reads_off_target`
\|\|	frag_size_mean	frag_size_mean	`seqtool-frag_size_mean`
\|\|	frag_size_std	frag_size_std	`seqtool-frag_size_std`
\|\|	dupes	dupes	`seqtool-dupes`
\|\|	n_q20	n_q20	`seqtool-n_q20`
\|\|	n_q25	n_q25	`seqtool-n_q25`
\|\|	n_q30	n_q30	`seqtool-n_q30`
\|\|	n_bases	n_bases	`seqtool-n_bases`

Depth Stats - coding_depth

Depth and read QC statistics for coding_depth panel.

Showing ⁴/₄ rows and ²⁶/₂₆ columns.

Sample Name	reads	unmapped	unique_reads	frac_dupes	pairs	frac_reads_off_target	frac_pairs_off_target	frag_size_q20	frag_size_median	frag_size_q80	proper_pairs	frac_proper_pairs	pairs_on_target	pairs_off_target	reads_on_target	reads_off_target	frag_size_mean	frag_size_std	dupes	n_q20	n_q25	n_q30	n_bases
HCC1395_BL.md	999992.0	9.0	853439.0	0.1	426713.0	1.0	1.0	164.0	275.0	427.0	426416.0	1.0	18295.0	408121.0	25965.0	827465.0	301.6	123.6	146553.0	1.0	0.9	0.9	144359392.0
HCC1395_tumor.md	999980.0	4.0	830860.0	0.2	415427.0	1.0	1.0	159.0	265.0	414.0	414949.0	1.0	15407.0	399542.0	22060.0	808796.0	291.9	119.9	169120.0	1.0	0.9	0.9	143959508.0
Sig_18_Blood.md	999982.0	7.0	884407.0	0.1	442197.0	1.0	1.0	168.0	280.0	436.0	441978.0	1.0	19564.0	422414.0	27104.0	857296.0	307.4	125.7	115575.0	1.0	0.9	0.9	144973902.0
Sig_18_tissue.md	999980.0	8.0	915604.0	0.1	457797.0	1.0	1.0	138.0	218.0	335.0	457316.0	1.0	19755.0	437561.0	31482.0	884114.0	241.9	94.9	84376.0	1.0	1.0	1.0	141505598.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: seqtool_depth_stats_altera_v3_targets_coding_postQC_hg38_bed_table

Sort	Column	Description	ID
\|\|	reads	reads	`seqtool-reads`
\|\|	unmapped	unmapped	`seqtool-unmapped`
\|\|	frac_unmapped	frac_unmapped	`seqtool-frac_unmapped`
\|\|	unique_reads	unique_reads	`seqtool-unique_reads`
\|\|	frac_dupes	frac_dupes	`seqtool-frac_dupes`
\|\|	pairs	pairs	`seqtool-pairs`
\|\|	frac_reads_on_target	frac_reads_on_target	`seqtool-frac_reads_on_target`
\|\|	frac_reads_off_target	frac_reads_off_target	`seqtool-frac_reads_off_target`
\|\|	frac_pairs_on_target	frac_pairs_on_target	`seqtool-frac_pairs_on_target`
\|\|	frac_pairs_off_target	frac_pairs_off_target	`seqtool-frac_pairs_off_target`
\|\|	frag_size_q20	frag_size_q20	`seqtool-frag_size_q20`
\|\|	frag_size_median	frag_size_median	`seqtool-frag_size_median`
\|\|	frag_size_q80	frag_size_q80	`seqtool-frag_size_q80`
\|\|	proper_pairs	proper_pairs	`seqtool-proper_pairs`
\|\|	frac_proper_pairs	frac_proper_pairs	`seqtool-frac_proper_pairs`
\|\|	pairs_on_target	pairs_on_target	`seqtool-pairs_on_target`
\|\|	pairs_off_target	pairs_off_target	`seqtool-pairs_off_target`
\|\|	reads_on_target	reads_on_target	`seqtool-reads_on_target`
\|\|	reads_off_target	reads_off_target	`seqtool-reads_off_target`
\|\|	frag_size_mean	frag_size_mean	`seqtool-frag_size_mean`
\|\|	frag_size_std	frag_size_std	`seqtool-frag_size_std`
\|\|	dupes	dupes	`seqtool-dupes`
\|\|	n_q20	n_q20	`seqtool-n_q20`
\|\|	n_q25	n_q25	`seqtool-n_q25`
\|\|	n_q30	n_q30	`seqtool-n_q30`
\|\|	n_bases	n_bases	`seqtool-n_bases`

Depth Stats - noncoding_depth

Depth and read QC statistics for noncoding_depth panel.

Showing ⁴/₄ rows and ²⁶/₂₆ columns.

Sample Name	reads	unmapped	unique_reads	frac_dupes	pairs	frac_reads_on_target	frac_reads_off_target	frac_pairs_on_target	frac_pairs_off_target	frag_size_q20	frag_size_median	frag_size_q80	proper_pairs	frac_proper_pairs	pairs_on_target	pairs_off_target	reads_on_target	reads_off_target	frag_size_mean	frag_size_std	dupes	n_q20	n_q25	n_q30	n_bases
HCC1395_BL.md	999992.0	9.0	853439.0	0.1	426713.0	0.2	0.8	0.2	0.8	164.0	275.0	427.0	426416.0	1.0	105842.0	320574.0	202363.0	651067.0	301.6	123.6	146553.0	1.0	0.9	0.9	144359392.0
HCC1395_tumor.md	999980.0	4.0	830860.0	0.2	415427.0	0.2	0.8	0.2	0.8	159.0	265.0	414.0	414949.0	1.0	94436.0	320513.0	181234.0	649622.0	291.9	119.9	169120.0	1.0	0.9	0.9	143959508.0
Sig_18_Blood.md	999982.0	7.0	884407.0	0.1	442197.0	0.3	0.7	0.3	0.7	168.0	280.0	436.0	441978.0	1.0	119108.0	322870.0	227917.0	656483.0	307.4	125.7	115575.0	1.0	0.9	0.9	144973902.0
Sig_18_tissue.md	999980.0	8.0	915604.0	0.1	457797.0	0.3	0.7	0.3	0.7	138.0	218.0	335.0	457316.0	1.0	121799.0	335517.0	236495.0	679101.0	241.9	94.9	84376.0	1.0	1.0	1.0	141505598.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: seqtool_depth_stats_altera_v3_targets_noncoding_postQC_hg38_bed_table

Sort	Column	Description	ID
\|\|	reads	reads	`seqtool-reads`
\|\|	unmapped	unmapped	`seqtool-unmapped`
\|\|	frac_unmapped	frac_unmapped	`seqtool-frac_unmapped`
\|\|	unique_reads	unique_reads	`seqtool-unique_reads`
\|\|	frac_dupes	frac_dupes	`seqtool-frac_dupes`
\|\|	pairs	pairs	`seqtool-pairs`
\|\|	frac_reads_on_target	frac_reads_on_target	`seqtool-frac_reads_on_target`
\|\|	frac_reads_off_target	frac_reads_off_target	`seqtool-frac_reads_off_target`
\|\|	frac_pairs_on_target	frac_pairs_on_target	`seqtool-frac_pairs_on_target`
\|\|	frac_pairs_off_target	frac_pairs_off_target	`seqtool-frac_pairs_off_target`
\|\|	frag_size_q20	frag_size_q20	`seqtool-frag_size_q20`
\|\|	frag_size_median	frag_size_median	`seqtool-frag_size_median`
\|\|	frag_size_q80	frag_size_q80	`seqtool-frag_size_q80`
\|\|	proper_pairs	proper_pairs	`seqtool-proper_pairs`
\|\|	frac_proper_pairs	frac_proper_pairs	`seqtool-frac_proper_pairs`
\|\|	pairs_on_target	pairs_on_target	`seqtool-pairs_on_target`
\|\|	pairs_off_target	pairs_off_target	`seqtool-pairs_off_target`
\|\|	reads_on_target	reads_on_target	`seqtool-reads_on_target`
\|\|	reads_off_target	reads_off_target	`seqtool-reads_off_target`
\|\|	frag_size_mean	frag_size_mean	`seqtool-frag_size_mean`
\|\|	frag_size_std	frag_size_std	`seqtool-frag_size_std`
\|\|	dupes	dupes	`seqtool-dupes`
\|\|	n_q20	n_q20	`seqtool-n_q20`
\|\|	n_q25	n_q25	`seqtool-n_q25`
\|\|	n_q30	n_q30	`seqtool-n_q30`
\|\|	n_bases	n_bases	`seqtool-n_bases`

Depth Stats - non_boosted_depth

Depth and read QC statistics for non_boosted_depth panel.

Showing ⁴/₄ rows and ²⁶/₂₆ columns.

Sample Name	reads	unmapped	unique_reads	frac_dupes	pairs	frac_reads_on_target	frac_reads_off_target	frac_pairs_on_target	frac_pairs_off_target	frag_size_q20	frag_size_median	frag_size_q80	proper_pairs	frac_proper_pairs	pairs_on_target	pairs_off_target	reads_on_target	reads_off_target	frag_size_mean	frag_size_std	dupes	n_q20	n_q25	n_q30	n_bases
HCC1395_BL.md	999992.0	9.0	853439.0	0.1	426713.0	0.4	0.6	0.5	0.5	164.0	275.0	427.0	426416.0	1.0	221377.0	205039.0	362511.0	490919.0	301.6	123.6	146553.0	1.0	0.9	0.9	144359392.0
HCC1395_tumor.md	999980.0	4.0	830860.0	0.2	415427.0	0.4	0.6	0.5	0.5	159.0	265.0	414.0	414949.0	1.0	223687.0	191262.0	370247.0	460609.0	291.9	119.9	169120.0	1.0	0.9	0.9	143959508.0
Sig_18_Blood.md	999982.0	7.0	884407.0	0.1	442197.0	0.4	0.6	0.5	0.5	168.0	280.0	436.0	441978.0	1.0	225144.0	216834.0	365965.0	518435.0	307.4	125.7	115575.0	1.0	0.9	0.9	144973902.0
Sig_18_tissue.md	999980.0	8.0	915604.0	0.1	457797.0	0.5	0.5	0.5	0.5	138.0	218.0	335.0	457316.0	1.0	242046.0	215270.0	428259.0	487337.0	241.9	94.9	84376.0	1.0	1.0	1.0	141505598.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: seqtool_depth_stats_xgen_exome_hyb_panel_v2_targets_hg38_minus_altera_v3_targets_postQC_hg38_bed_table

Sort	Column	Description	ID
\|\|	reads	reads	`seqtool-reads`
\|\|	unmapped	unmapped	`seqtool-unmapped`
\|\|	frac_unmapped	frac_unmapped	`seqtool-frac_unmapped`
\|\|	unique_reads	unique_reads	`seqtool-unique_reads`
\|\|	frac_dupes	frac_dupes	`seqtool-frac_dupes`
\|\|	pairs	pairs	`seqtool-pairs`
\|\|	frac_reads_on_target	frac_reads_on_target	`seqtool-frac_reads_on_target`
\|\|	frac_reads_off_target	frac_reads_off_target	`seqtool-frac_reads_off_target`
\|\|	frac_pairs_on_target	frac_pairs_on_target	`seqtool-frac_pairs_on_target`
\|\|	frac_pairs_off_target	frac_pairs_off_target	`seqtool-frac_pairs_off_target`
\|\|	frag_size_q20	frag_size_q20	`seqtool-frag_size_q20`
\|\|	frag_size_median	frag_size_median	`seqtool-frag_size_median`
\|\|	frag_size_q80	frag_size_q80	`seqtool-frag_size_q80`
\|\|	proper_pairs	proper_pairs	`seqtool-proper_pairs`
\|\|	frac_proper_pairs	frac_proper_pairs	`seqtool-frac_proper_pairs`
\|\|	pairs_on_target	pairs_on_target	`seqtool-pairs_on_target`
\|\|	pairs_off_target	pairs_off_target	`seqtool-pairs_off_target`
\|\|	reads_on_target	reads_on_target	`seqtool-reads_on_target`
\|\|	reads_off_target	reads_off_target	`seqtool-reads_off_target`
\|\|	frag_size_mean	frag_size_mean	`seqtool-frag_size_mean`
\|\|	frag_size_std	frag_size_std	`seqtool-frag_size_std`
\|\|	dupes	dupes	`seqtool-dupes`
\|\|	n_q20	n_q20	`seqtool-n_q20`
\|\|	n_q25	n_q25	`seqtool-n_q25`
\|\|	n_q30	n_q30	`seqtool-n_q30`
\|\|	n_bases	n_bases	`seqtool-n_bases`

Depth Stats - hotspot_depth

Depth and read QC statistics for hotspot_depth panel.

Showing ⁴/₄ rows and ²⁶/₂₆ columns.

Sample Name	reads	unmapped	unique_reads	frac_dupes	pairs	frac_reads_off_target	frac_pairs_off_target	frag_size_q20	frag_size_median	frag_size_q80	proper_pairs	frac_proper_pairs	pairs_off_target	reads_off_target	frag_size_mean	frag_size_std	dupes	n_q20	n_q25	n_q30	n_bases
HCC1395_BL.md	999992.0	9.0	853439.0	0.1	426713.0	1.0	1.0	164.0	275.0	427.0	426416.0	1.0	426416.0	853430.0	301.6	123.6	146553.0	1.0	0.9	0.9	144359392.0
HCC1395_tumor.md	999980.0	4.0	830860.0	0.2	415427.0	1.0	1.0	159.0	265.0	414.0	414949.0	1.0	414949.0	830856.0	291.9	119.9	169120.0	1.0	0.9	0.9	143959508.0
Sig_18_Blood.md	999982.0	7.0	884407.0	0.1	442197.0	1.0	1.0	168.0	280.0	436.0	441978.0	1.0	441978.0	884400.0	307.4	125.7	115575.0	1.0	0.9	0.9	144973902.0
Sig_18_tissue.md	999980.0	8.0	915604.0	0.1	457797.0	1.0	1.0	138.0	218.0	335.0	457316.0	1.0	457316.0	915596.0	241.9	94.9	84376.0	1.0	1.0	1.0	141505598.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: seqtool_depth_stats_FINAL_hotspot_list_07302025_hg38_sorted_bed_table

Sort	Column	Description	ID
\|\|	reads	reads	`seqtool-reads`
\|\|	unmapped	unmapped	`seqtool-unmapped`
\|\|	frac_unmapped	frac_unmapped	`seqtool-frac_unmapped`
\|\|	unique_reads	unique_reads	`seqtool-unique_reads`
\|\|	frac_dupes	frac_dupes	`seqtool-frac_dupes`
\|\|	pairs	pairs	`seqtool-pairs`
\|\|	frac_reads_on_target	frac_reads_on_target	`seqtool-frac_reads_on_target`
\|\|	frac_reads_off_target	frac_reads_off_target	`seqtool-frac_reads_off_target`
\|\|	frac_pairs_on_target	frac_pairs_on_target	`seqtool-frac_pairs_on_target`
\|\|	frac_pairs_off_target	frac_pairs_off_target	`seqtool-frac_pairs_off_target`
\|\|	frag_size_q20	frag_size_q20	`seqtool-frag_size_q20`
\|\|	frag_size_median	frag_size_median	`seqtool-frag_size_median`
\|\|	frag_size_q80	frag_size_q80	`seqtool-frag_size_q80`
\|\|	proper_pairs	proper_pairs	`seqtool-proper_pairs`
\|\|	frac_proper_pairs	frac_proper_pairs	`seqtool-frac_proper_pairs`
\|\|	pairs_on_target	pairs_on_target	`seqtool-pairs_on_target`
\|\|	pairs_off_target	pairs_off_target	`seqtool-pairs_off_target`
\|\|	reads_on_target	reads_on_target	`seqtool-reads_on_target`
\|\|	reads_off_target	reads_off_target	`seqtool-reads_off_target`
\|\|	frag_size_mean	frag_size_mean	`seqtool-frag_size_mean`
\|\|	frag_size_std	frag_size_std	`seqtool-frag_size_std`
\|\|	dupes	dupes	`seqtool-dupes`
\|\|	n_q20	n_q20	`seqtool-n_q20`
\|\|	n_q25	n_q25	`seqtool-n_q25`
\|\|	n_q30	n_q30	`seqtool-n_q30`
\|\|	n_bases	n_bases	`seqtool-n_bases`

Depth Stats - foresight_depth

Depth and read QC statistics for foresight_depth panel.

Showing ⁴/₄ rows and ²⁶/₂₆ columns.

Sample Name	reads	unmapped	unique_reads	frac_dupes	pairs	frac_reads_off_target	frac_pairs_off_target	frag_size_q20	frag_size_median	frag_size_q80	proper_pairs	frac_proper_pairs	pairs_on_target	pairs_off_target	reads_on_target	reads_off_target	frag_size_mean	frag_size_std	dupes	n_q20	n_q25	n_q30	n_bases
HCC1395_BL.md	999992.0	9.0	853439.0	0.1	426713.0	1.0	1.0	164.0	275.0	427.0	426416.0	1.0	4124.0	422292.0	6791.0	846639.0	301.6	123.6	146553.0	1.0	0.9	0.9	144359392.0
HCC1395_tumor.md	999980.0	4.0	830860.0	0.2	415427.0	1.0	1.0	159.0	265.0	414.0	414949.0	1.0	3614.0	411335.0	5971.0	824885.0	291.9	119.9	169120.0	1.0	0.9	0.9	143959508.0
Sig_18_Blood.md	999982.0	7.0	884407.0	0.1	442197.0	1.0	1.0	168.0	280.0	436.0	441978.0	1.0	4003.0	437975.0	6498.0	877902.0	307.4	125.7	115575.0	1.0	0.9	0.9	144973902.0
Sig_18_tissue.md	999980.0	8.0	915604.0	0.1	457797.0	1.0	1.0	138.0	218.0	335.0	457316.0	1.0	3990.0	453326.0	7086.0	908510.0	241.9	94.9	84376.0	1.0	1.0	1.0	141505598.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: seqtool_depth_stats_foresight_clarity_targets_hg38_bed_table

Sort	Column	Description	ID
\|\|	reads	reads	`seqtool-reads`
\|\|	unmapped	unmapped	`seqtool-unmapped`
\|\|	frac_unmapped	frac_unmapped	`seqtool-frac_unmapped`
\|\|	unique_reads	unique_reads	`seqtool-unique_reads`
\|\|	frac_dupes	frac_dupes	`seqtool-frac_dupes`
\|\|	pairs	pairs	`seqtool-pairs`
\|\|	frac_reads_on_target	frac_reads_on_target	`seqtool-frac_reads_on_target`
\|\|	frac_reads_off_target	frac_reads_off_target	`seqtool-frac_reads_off_target`
\|\|	frac_pairs_on_target	frac_pairs_on_target	`seqtool-frac_pairs_on_target`
\|\|	frac_pairs_off_target	frac_pairs_off_target	`seqtool-frac_pairs_off_target`
\|\|	frag_size_q20	frag_size_q20	`seqtool-frag_size_q20`
\|\|	frag_size_median	frag_size_median	`seqtool-frag_size_median`
\|\|	frag_size_q80	frag_size_q80	`seqtool-frag_size_q80`
\|\|	proper_pairs	proper_pairs	`seqtool-proper_pairs`
\|\|	frac_proper_pairs	frac_proper_pairs	`seqtool-frac_proper_pairs`
\|\|	pairs_on_target	pairs_on_target	`seqtool-pairs_on_target`
\|\|	pairs_off_target	pairs_off_target	`seqtool-pairs_off_target`
\|\|	reads_on_target	reads_on_target	`seqtool-reads_on_target`
\|\|	reads_off_target	reads_off_target	`seqtool-reads_off_target`
\|\|	frag_size_mean	frag_size_mean	`seqtool-frag_size_mean`
\|\|	frag_size_std	frag_size_std	`seqtool-frag_size_std`
\|\|	dupes	dupes	`seqtool-dupes`
\|\|	n_q20	n_q20	`seqtool-n_q20`
\|\|	n_q25	n_q25	`seqtool-n_q25`
\|\|	n_q30	n_q30	`seqtool-n_q30`
\|\|	n_bases	n_bases	`seqtool-n_bases`

Fragment Size

Fragment size statistics.

Showing ⁴/₄ rows and ⁸/₈ columns.

Sample Name	fragment_size_mean	fragment_size_median	fragment_size_std	fragment_size_q10	fragment_size_q25	fragment_size_q50	fragment_size_q75	fragment_size_q90
HCC1395_BL.md	111.4	103.5	74.9	5.7	85.5	103.5	120.2	196.2
HCC1395_tumor.md	131.4	115.5	109.3	0.0	70.5	115.5	147.5	321.0
Sig_18_Blood.md	178.4	126.5	138.6	77.0	94.8	126.5	212.0	384.0
Sig_18_tissue.md	106.2	100.0	97.2	0.0	0.0	100.0	131.5	220.0

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

Sort	Column	Description	ID
\|\|	fragment_size_mean	fragment_size_mean	`seqtool-fragment_size_mean`
\|\|	fragment_size_median	fragment_size_median	`seqtool-fragment_size_median`
\|\|	fragment_size_std	fragment_size_std	`seqtool-fragment_size_std`
\|\|	fragment_size_q10	fragment_size_q10	`seqtool-fragment_size_q10`
\|\|	fragment_size_q25	fragment_size_q25	`seqtool-fragment_size_q25`
\|\|	fragment_size_q50	fragment_size_q50	`seqtool-fragment_size_q50`
\|\|	fragment_size_q75	fragment_size_q75	`seqtool-fragment_size_q75`
\|\|	fragment_size_q90	fragment_size_q90	`seqtool-fragment_size_q90`

GC Bias

GC bias plot by panel.

Created with MultiQC

Mosdepth

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.https://github.com/brentp/mosdepthDOI: 10.1093/bioinformatics/btx699

Cumulative coverage distribution

Proportion of bases in the reference genome with, at least, a given depth of coverage. Note that for 4 samples, a BED file was provided, so the data was calculated across those regions. For 4 samples, it's calculated across the entire genome length. 4 samples have both global and region reports, and we are showing the data for regions

For a set of DNA or RNA reads mapped to a reference sequence, such as a genome or transcriptome, the depth of coverage at a given base position is the number of high-quality reads that map to the reference at that position, while the breadth of coverage is the fraction of the reference sequence to which reads have been mapped with at least a given depth of coverage (Sims et al. 2014).

Defining coverage breadth in terms of coverage depth is useful, because sequencing experiments typically require a specific minimum depth of coverage over the region of interest (Sims et al. 2014), so the extent of the reference sequence that is amenable to analysis is constrained to lie within regions that have sufficient depth. With inadequate sequencing breadth, it can be difficult to distinguish the absence of a biological feature (such as a gene) from a lack of data (Green 2007).

For increasing coverage depths (1×, 2×, …, N×), coverage breadth is calculated as the percentage of the reference sequence that is covered by at least that number of reads, then plots coverage breadth (y-axis) against coverage depth (x-axis). This plot shows the relationship between sequencing depth and breadth for each read dataset, which can be used to gauge, for example, the likely effect of a minimum depth filter on the fraction of a genome available for analysis.

Created with MultiQC

Average coverage per contig

Average coverage per contig or chromosome

Created with MultiQC

XY coverage

Created with MultiQC

Picard

Tools for manipulating high-throughput sequencing data.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.

Alignment summary metrics from Sentieon (Picard format)

Created with MultiQC

Mean read length

The mean read length of the set of reads examined.

Created with MultiQC

Hybrid-selection metrics

Parsed from Picard HsMetrics tool that takes a SAM/BAM file input and collects metrics that are specific for sequence datasets generated through hybrid-selection. Hybrid-selection (HS) is the most commonly used technique to capture exon-specific sequences for targeted sequencing experiments such as exome sequencing.

Hybrid selection metrics from Sentieon (Picard format)

Showing ⁴/₄ rows and ¹⁹/₂₄ columns.

Sample Name	At dropout	Bait design efficiency	Bait territory	Fold enrichment	Gc dropout	Near-bait bases	Off-bait bases	On-bait bases	On-target bases	Usable bases on-bait	Usable bases on-target	PF bases aligned	PF reads	Selected bases	PF unique reads	PF unique bases aligned	PF unique reads aligned	Total reads	Mean bait coverage	Mean target coverage	On-bait vs selected	Target territory	Zero coverage targets
HCC1395_BL	20.5	1.0	46390665.0	39.4	10.0	30.2Mb	32.1Mb	81.8Mb	54.5Mb	56.6%	37.7%	144.0Mb	1.0M	77.7%	0.9M	122.6Mb	0.9M	1.0M	1.8	1.2	0.7	46390665.0	99.0%
HCC1395_tumor	19.8	1.0	46390665.0	39.0	8.3	30.4Mb	32.5Mb	80.6Mb	52.1Mb	56.0%	36.2%	143.5Mb	1.0M	77.4%	0.8M	118.9Mb	0.8M	1.0M	1.7	1.1	0.7	46390665.0	99.0%
Sig_18_Blood	20.1	1.0	46390665.0	39.5	12.0	31.0Mb	31.2Mb	82.5Mb	58.2Mb	56.9%	40.2%	144.6Mb	1.0M	78.4%	0.9M	127.6Mb	0.9M	1.0M	1.8	1.3	0.7	46390665.0	99.0%
Sig_18_tissue	20.2	1.0	46390665.0	43.2	10.9	26.6Mb	26.7Mb	88.0Mb	62.6Mb	62.2%	44.2%	141.2Mb	1.0M	81.1%	0.9M	129.0Mb	0.9M	1.0M	1.9	1.3	0.8	46390665.0	99.0%

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

Sort	Column	Description	ID	Scale
\|\|	At dropout	A measure of how undercovered <= 50% GC regions are relative to the mean.	`hsmetrics-AT_DROPOUT`
\|\|	Bait design efficiency	Target territory / bait territory. 1 == perfectly efficient, 0.5 = half of baited bases are not target.	`hsmetrics-BAIT_DESIGN_EFFICIENCY`
\|\|	Bait territory	The number of bases which have one or more baits on top of them.	`hsmetrics-BAIT_TERRITORY`
\|\|	Fold 80 base penalty	The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.	`hsmetrics-FOLD_80_BASE_PENALTY`
\|\|	Fold enrichment	The fold by which the baited region has been amplified above genomic background.	`hsmetrics-FOLD_ENRICHMENT`
\|\|	Gc dropout	A measure of how undercovered >= 50% GC regions are relative to the mean.	`hsmetrics-GC_DROPOUT`
\|\|	Near-bait bases	The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region.	`hsmetrics-NEAR_BAIT_BASES`	base_count
\|\|	Off-bait bases	The number of PF aligned bases that mapped to neither on or near a bait.	`hsmetrics-OFF_BAIT_BASES`	base_count
\|\|	On-bait bases	The number of PF aligned bases that mapped to a baited region of the genome.	`hsmetrics-ON_BAIT_BASES`	base_count
\|\|	On-target bases	The number of PF aligned bases that mapped to a targeted region of the genome.	`hsmetrics-ON_TARGET_BASES`	base_count
\|\|	Usable bases on-bait	The number of aligned, de-duped, on-bait bases out of the PF bases available.	`hsmetrics-PCT_USABLE_BASES_ON_BAIT`
\|\|	Usable bases on-target	The number of aligned, de-duped, on-target bases out of the PF bases available.	`hsmetrics-PCT_USABLE_BASES_ON_TARGET`
\|\|	PF bases aligned	The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.	`hsmetrics-PF_BASES_ALIGNED`	base_count
\|\|	PF reads	The number of reads that pass the vendor's filter.	`hsmetrics-PF_READS`	read_count
\|\|	Selected bases	On+Near Bait Bases / PF Bases Aligned.	`hsmetrics-PCT_SELECTED_BASES`
\|\|	PF unique reads	The number of PF reads that are not marked as duplicates.	`hsmetrics-PF_UNIQUE_READS`	read_count
\|\|	PF unique bases aligned	The number of bases in the PF aligned reads that are mapped to a reference base. Accounts for clipping and gaps.	`hsmetrics-PF_UQ_BASES_ALIGNED`	base_count
\|\|	PF unique reads aligned	The number of PF unique reads that are aligned with mapping score > 0 to the reference genome.	`hsmetrics-PF_UQ_READS_ALIGNED`	read_count
\|\|	Total reads	The total number of reads in the SAM or BAM file examine.	`hsmetrics-TOTAL_READS`	read_count
\|\|	Mean bait coverage	The mean coverage of all baits in the experiment.	`hsmetrics-MEAN_BAIT_COVERAGE`
\|\|	Mean target coverage	The mean coverage of targets.	`hsmetrics-MEAN_TARGET_COVERAGE`
\|\|	On-bait vs selected	The percentage of on+near bait bases that are on as opposed to near.	`hsmetrics-ON_BAIT_VS_SELECTED`
\|\|	Target territory	The unique number of target bases in the experiment where target is usually exons etc.	`hsmetrics-TARGET_TERRITORY`
\|\|	Zero coverage targets	The fraction of targets that did not reach coverage=1 over any base.	`hsmetrics-ZERO_CVG_TARGETS_PCT`

Hybrid-selection target coverage

The percentage of all target bases with at least x fold coverage.

Created with MultiQC

Hybrid-selection penalty

The "hybrid selection penalty" incurred to get 80% of target bases to a given coverage.

Can be used with the following formula:

required_aligned_bases = bait_size_bp * desired_coverage * hs_penalty

Created with MultiQC

Insert Size

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

Insert size distribution from Sentieon (Picard format)

Created with MultiQC

Mark Duplicates

Number of reads, categorised by duplication state. Pair counts are doubled - see help text for details.

Duplicate marking metrics from Sentieon MarkDuplicates

The table in the Picard metrics file contains some columns referring read pairs and some referring to single reads.

To make the numbers in this plot sum correctly, values referring to pairs are doubled according to the scheme below:

READS_IN_DUPLICATE_PAIRS = 2 * READ_PAIR_DUPLICATES
READS_IN_UNIQUE_PAIRS = 2 * (READ_PAIRS_EXAMINED - READ_PAIR_DUPLICATES)
READS_IN_UNIQUE_UNPAIRED = UNPAIRED_READS_EXAMINED - UNPAIRED_READ_DUPLICATES
READS_IN_DUPLICATE_PAIRS_OPTICAL = 2 * READ_PAIR_OPTICAL_DUPLICATES
READS_IN_DUPLICATE_PAIRS_NONOPTICAL = READS_IN_DUPLICATE_PAIRS - READS_IN_DUPLICATE_PAIRS_OPTICAL
READS_IN_DUPLICATE_UNPAIRED = UNPAIRED_READ_DUPLICATES
READS_UNMAPPED = UNMAPPED_READS

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

Samtools

Version:


                      
                        1.21

HTSlib:


                      
                        1.23

Toolkit for interacting with BAM/CRAM files.http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

Percent mapped

Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.

For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.

Created with MultiQC

Alignment stats

This module parses the output from samtools stats. All numbers in millions.

Alignment statistics from samtools stats on post-dedup BAMs

Created with MultiQC

Sample Name	Total sequences	Mapped & paired	Properly paired	Duplicated	QC Failed	Reads MQ0	Mapped bases (CIGAR)	Bases Trimmed	Duplicated bases	Diff chromosomes	Other orientation	Inward pairs	Outward pairs
HCC1395_BL	1.0M	1.0M	1.0M	0.1M	0.0M	0.1M	144.0Mb	0.0Mb	21.4Mb	0.0M	0.0M	0.5M	0.0M
HCC1395_tumor	1.0M	1.0M	1.0M	0.2M	0.0M	0.1M	143.5Mb	0.0Mb	24.7Mb	0.0M	0.0M	0.5M	0.0M
Sig_18_Blood	1.0M	1.0M	1.0M	0.1M	0.0M	0.1M	144.6Mb	0.0Mb	17.1Mb	0.0M	0.0M	0.5M	0.0M
Sig_18_tissue	1.0M	1.0M	1.0M	0.1M	0.0M	0.1M	141.2Mb	0.0Mb	12.3Mb	0.0M	0.0M	0.4M	0.1M

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samtools-stats-dp_table

Sort	Column	Description	ID	Scale
\|\|	Total sequences	Total sequences	`raw_total_sequences`	read_count
\|\|	Mapped & paired	Paired-end technology bit set + both mates mapped	`reads_mapped_and_paired`	read_count
\|\|	Properly paired	Proper-pair bit set	`reads_properly_paired`	read_count
\|\|	Duplicated	PCR or optical duplicate bit set	`reads_duplicated`	read_count
\|\|	QC Failed	QC Failed	`reads_QC_failed`	read_count
\|\|	Reads MQ0	Reads mapped and MQ=0	`reads_MQ0`	read_count
\|\|	Mapped bases (CIGAR)	Mapped bases (CIGAR)	`bases_mapped__cigar`	base_count
\|\|	Bases Trimmed	Bases Trimmed	`bases_trimmed`	base_count
\|\|	Duplicated bases	Duplicated bases	`bases_duplicated`	base_count
\|\|	Diff chromosomes	Pairs on different chromosomes	`pairs_on_different_chromosomes`	read_count
\|\|	Other orientation	Pairs with other orientation	`pairs_with_other_orientation`	read_count
\|\|	Inward pairs	Inward oriented pairs	`inward_oriented_pairs`	read_count
\|\|	Outward pairs	Outward oriented pairs	`outward_oriented_pairs`	read_count

fastp

Version:


                      
                        1.0.1

All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

Pre-alignment QC and adapter trimming, run per sample

Filtered Reads

Filtering statistics of sampled reads.

Created with MultiQC

Insert Sizes

Insert size estimation of sampled reads.

Created with MultiQC

Sequence Quality

Average sequencing quality over each base of all reads.

Created with MultiQC

GC Content

Average GC content over each base of all reads.

Created with MultiQC

N content

Average N content over each base of all reads.

Created with MultiQC

Software Versions

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

Group	Software	Version
Samtools	HTSlib	`1.23`
	Samtools	`1.21`
fastp	fastp	`1.0.1`

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General Statistics

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Seqtool

Basic Stats

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Seqtool: Full Basic Stats: Columns

Depth Stats - all_targets

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Seqtool: Depth Stats - all_targets: Columns

Depth Stats - all_probes

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Seqtool: Depth Stats - all_probes: Columns

Depth Stats - boosted_depth

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Seqtool: Depth Stats - boosted_depth: Columns

Depth Stats - coding_depth

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Seqtool: Depth Stats - coding_depth: Columns

Depth Stats - noncoding_depth

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Seqtool: Depth Stats - noncoding_depth: Columns

Depth Stats - non_boosted_depth

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Seqtool: Depth Stats - non_boosted_depth: Columns

Depth Stats - hotspot_depth

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Seqtool: Depth Stats - hotspot_depth: Columns

Depth Stats - foresight_depth

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Seqtool: Depth Stats - foresight_depth: Columns

Fragment Size

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Seqtool: Fragment Size: Columns

GC Bias

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Mosdepth

Cumulative coverage distribution Help

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Average coverage per contig

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XY coverage

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Picard

Alignment Summary

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Mean read length

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Hybrid-selection metrics

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Picard HsMetrics: Columns

Hybrid-selection target coverage

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Hybrid-selection penalty Help

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Insert Size

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Mean Base Quality by Cycle Help

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Base Quality Distribution

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