PCRpanel amplicon sequencing QC (DRAGEN, hg38)

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

Metrics generated using DRAGEN v4.4.4 07.031.779 (0x18101306) (hg38 pangenome v5)

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Report generated on 2026-07-27, 15:46 +05 based on data in: /staging/adaniyarov/target_panel_project/251205_M03068_0097_000000000-DVCJ3/gvcf_hg38_v11_pangenome_v5

General Statistics

Showing ¹⁶/₁₆ rows and ⁸/₄₉ columns.

Sample Name	M Input reads	Paired	QC-fail	Map	Unmap	Dup	Prop pair	Discord	Diff chr, MQ⩾10	Med IS	Q30	M Alignments	Sec'ry	Suppl'ry	Reads on target BED	Reads on target WGS	Bases on target BED	Bases on target WGS	Depth BED	Depth WGS	Uniformity(>0.2×mean) BED	Uniformity(>0.2×mean) WGS	Uniformity(>0.4×mean) BED	Uniformity(>0.4×mean) WGS	Med aut cov BED	Med aut cov WGS	≥1500x BED	≥1000x BED	≥500x BED	≥100x BED	≥50x BED	≥20x BED	≥15x BED	≥10x BED	≥3x BED	≥1x BED	≥0x BED	≥1500x WGS	≥1000x WGS	≥500x WGS	≥100x WGS	≥50x WGS	≥20x WGS	≥15x WGS	≥10x WGS	≥3x WGS	≥1x WGS	≥0x WGS	% GC
Alp13-1-20 \| Alp13-1-20	0.1M	100.0%	0.00%	97.5%	2.5%	0.0%	93.1%	3.77%	0.07%	217	95.9%	0.1M	0.00%	0.13%	83.0%	100.0%	59.2%	100.0%	258.71x	0.01x	8.64%	0.00%	8.64%	0.00%	3658.50x	0.00x	5.43%	6.85%	8.01%	8.64%	8.64%	8.64%	8.64%	8.64%	9.10%	16.93%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	43%
Alp13-1-100 \| Alp13-1-100	0.1M	100.0%	0.00%	98.7%	1.3%	0.0%	95.2%	2.78%	0.06%	217	96.5%	0.1M	0.00%	0.15%	81.8%	100.0%	57.7%	100.0%	238.63x	0.01x	8.64%	0.00%	8.64%	0.00%	2955.00x	0.00x	5.65%	7.05%	8.12%	8.64%	8.64%	8.64%	8.64%	8.64%	8.95%	14.52%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	42%
Alp22-1-20 \| Alp22-1-20	0.1M	100.0%	0.00%	99.0%	0.9%	0.0%	97.7%	0.69%	0.07%	222	94.8%	0.1M	0.00%	0.14%	88.4%	100.0%	43.7%	100.0%	176.93x	0.01x	7.86%	0.01%	7.86%	0.01%	2024.00x	0.00x	4.46%	5.42%	7.08%	7.86%	7.86%	7.86%	7.86%	7.86%	8.72%	13.74%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	45%
Alp22-1-100 \| Alp22-1-100	0.1M	100.0%	0.00%	99.1%	0.9%	0.0%	94.9%	3.53%	0.06%	222	96.0%	0.1M	0.00%	0.13%	88.4%	100.0%	43.4%	100.0%	194.42x	0.01x	7.86%	0.01%	7.86%	0.01%	2191.00x	0.00x	4.70%	5.64%	7.13%	7.86%	7.86%	7.86%	7.86%	7.95%	8.44%	14.30%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	45%
Alp32-1-20 \| Alp32-1-20	0.1M	100.0%	0.00%	99.3%	0.7%	0.0%	98.2%	0.62%	0.08%	244	93.1%	0.1M	0.00%	0.03%	80.4%	100.0%	41.3%	100.0%	176.40x	0.01x	7.33%	0.01%	7.33%	0.01%	1.00x	0.00x	4.25%	5.16%	6.58%	7.11%	7.33%	7.33%	7.33%	7.33%	7.59%	12.63%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	51%
Alp32-1-100 \| Alp32-1-100	0.1M	100.0%	0.00%	99.2%	0.8%	0.0%	97.9%	0.73%	0.08%	244	93.0%	0.1M	0.00%	0.04%	80.5%	100.0%	41.2%	100.0%	156.76x	0.01x	7.33%	0.01%	7.33%	0.01%	1.00x	0.00x	3.65%	4.81%	6.20%	7.18%	7.33%	7.33%	7.33%	7.33%	8.05%	13.51%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	51%
Alp42-1-20 \| Alp42-1-20	0.1M	100.0%	0.00%	98.2%	1.8%	0.0%	92.1%	5.35%	0.08%	235	94.9%	0.1M	0.00%	0.03%	96.0%	100.0%	51.9%	100.0%	225.55x	0.01x	5.94%	0.01%	5.54%	0.01%	1.00x	0.00x	4.15%	4.76%	4.91%	5.54%	5.93%	5.94%	5.94%	5.94%	6.16%	13.01%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	55%
Alp42-1-100 \| Alp42-1-100	0.1M	100.0%	0.00%	98.3%	1.7%	0.0%	92.0%	5.42%	0.10%	235	95.7%	0.1M	0.00%	0.03%	96.1%	100.0%	52.1%	100.0%	210.69x	0.01x	5.94%	0.01%	5.54%	0.01%	1.00x	0.00x	3.59%	4.63%	4.76%	5.54%	5.92%	5.94%	5.94%	5.94%	6.33%	14.07%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	55%
Alp52-1-20 \| Alp52-1-20	0.1M	100.0%	0.00%	99.2%	0.8%	0.0%	96.2%	2.45%	0.06%	214	95.7%	0.1M	0.00%	0.03%	78.5%	100.0%	38.1%	100.0%	166.93x	0.01x	14.00%	0.01%	13.43%	0.01%	1053.00x	0.00x	3.12%	4.06%	7.72%	12.94%	13.95%	14.00%	14.00%	14.07%	14.13%	15.73%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	47%
Alp52-1-100 \| Alp52-1-100	0.1M	100.0%	0.00%	99.2%	0.8%	0.0%	95.4%	3.11%	0.06%	214	96.2%	0.1M	0.00%	0.03%	78.2%	100.0%	38.1%	100.0%	149.07x	0.01x	14.00%	0.01%	13.43%	0.01%	945.00x	0.00x	2.91%	3.64%	7.19%	12.65%	13.70%	14.00%	14.00%	14.12%	14.13%	19.00%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	47%
Alp62-1-20 \| Alp62-1-20	0.2M	100.0%	0.00%	98.8%	1.1%	0.0%	91.9%	6.21%	0.10%	220	95.8%	0.2M	0.00%	0.22%	82.7%	100.0%	53.2%	100.0%	273.65x	0.01x	10.17%	0.02%	10.17%	0.02%	3480.00x	0.00x	5.99%	6.94%	8.29%	10.17%	10.22%	10.34%	10.34%	10.34%	10.78%	16.34%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.02%	100.00%	48%
Alp62-1-100 \| Alp62-1-100	0.2M	100.0%	0.00%	98.8%	1.2%	0.0%	94.0%	3.87%	0.13%	223	96.2%	0.2M	0.00%	0.21%	82.3%	100.0%	53.2%	100.0%	264.53x	0.01x	10.17%	0.02%	10.17%	0.02%	3553.00x	0.00x	5.90%	7.18%	9.00%	10.17%	10.17%	10.23%	10.34%	10.34%	11.46%	17.63%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.02%	100.00%	47%
AlpP2-NG011977-1-20 \| AlpP2-NG011977-1-20	0.1M	100.0%	0.00%	94.2%	5.8%	0.0%	93.2%	0.22%	0.08%	245	94.8%	0.1M	0.00%	0.01%	77.8%	100.0%	47.5%	100.0%	197.19x	0.01x	2.23%	0.00%	2.23%	0.00%	1.00x	0.00x	2.12%	2.12%	2.16%	2.23%	2.23%	2.23%	2.23%	2.23%	2.70%	7.58%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	44%
AlpP2-NG011977-1-100 \| AlpP2-NG011977-1-100	0.1M	100.0%	0.00%	96.5%	3.5%	0.0%	48.0%	47.70%	0.07%	273	95.7%	0.1M	0.00%	0.00%	79.1%	100.0%	49.4%	100.0%	204.94x	0.01x	2.23%	0.00%	2.23%	0.00%	1.00x	0.00x	1.97%	2.12%	2.12%	2.22%	2.23%	2.23%	2.23%	2.23%	2.40%	8.83%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	43%
AlpP3-1-20 \| AlpP3-1-20	0.1M	100.0%	0.00%	94.9%	5.1%	0.0%	93.0%	1.27%	0.09%	222	95.3%	0.1M	0.00%	0.11%	72.5%	100.0%	22.2%	100.0%	92.50x	0.01x	1.55%	0.00%	1.55%	0.00%	1.00x	0.00x	1.55%	1.55%	1.55%	1.55%	1.55%	1.55%	1.55%	1.55%	2.13%	9.58%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	42%
AlpP3-1-100 \| AlpP3-1-100	0.1M	100.0%	0.00%	97.6%	2.4%	0.0%	96.1%	0.75%	0.08%	222	96.4%	0.1M	0.00%	0.17%	72.3%	100.0%	22.1%	100.0%	104.34x	0.01x	1.55%	0.00%	1.55%	0.00%	2.00x	0.00x	1.55%	1.55%	1.55%	1.55%	1.55%	1.55%	1.55%	1.55%	2.48%	10.53%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	42%

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
\|\|	DRAGEN: Mapping	M Input reads	Total number of input reads for this sample (or total number of reads in all input read groups combined), millions	`dragen_mapping-Total_input_reads`	read_count
\|\|	DRAGEN: Mapping	Paired	% of reads with a mate sequenced	`dragen_mapping-Reads_with_mate_sequenced_pct`
\|\|	DRAGEN: Mapping	QC-fail	% of reads not passing platform/vendor quality checks (SAM flag 0x200)	`dragen_mapping-QC_failed_reads_pct`
\|\|	DRAGEN: Mapping	Map	% of mapped reads	`dragen_mapping-Mapped_reads_pct`
\|\|	DRAGEN: Mapping	Unmap	% of unmapped reads	`dragen_mapping-Unmapped_reads_pct`
\|\|	DRAGEN: Mapping	Dup	% of duplicate marked reads as a result of the --enable-duplicatemarking option being used	`dragen_mapping-Number_of_duplicate_marked_reads_pct`
\|\|	DRAGEN: Mapping	Prop pair	% of properly paired reads (both reads in pair are mapped and fall within an acceptable range from each other based on the estimated insert length distribution). Duplicate and low quality reads are not excluded, i.e. the percentage is calculated relative to the total number of reads.	`dragen_mapping-Properly_paired_reads_pct`
\|\|	DRAGEN: Mapping	Discord	% of discordant reads: paired reads minus properly paired reads	`dragen_mapping-Not_properly_paired_reads_discordant_pct`
\|\|	DRAGEN: Mapping	Diff chr, MQ⩾10	% of paired reads, mapped with MAPQ>=10 and with a mate mapped to a different chromosome	`dragen_mapping-Paired_reads_mapped_to_different_chromosomes_MAPQ_10_pct`
\|\|	DRAGEN: Mapping	Med IS	Median insert size	`dragen_mapping-Insert_length_median`
\|\|	DRAGEN: Mapping	Q30	% of raw bases with BQ >= 30	`dragen_mapping-Q30_bases_pct`
\|\|	DRAGEN: Mapping	M Alignments	Total number of alignments with MQ > 0, millions	`dragen_mapping-Total_alignments`	read_count
\|\|	DRAGEN: Mapping	Sec'ry	% of secondary alignments. Secondary alignment occurs when a given read could align reasonably well to more than one place. One of the possible reported alignments is termed "primary" and the others will be marked as "secondary".	`dragen_mapping-Secondary_alignments_pct`
\|\|	DRAGEN: Mapping	Suppl'ry	% of supplementary (chimeric) alignments. A chimeric read is split over multiple loci (possibly due to structural variants). One alignment is referred to as the representative alignment, the other are supplementary	`dragen_mapping-Supplementary_chimeric_alignments_pct`
\|\|	DRAGEN: Coverage	Reads on target BED	Number of uniquely mapped reads to target region relative to the number of uniquely mapped reads to the genome.	`dragen_coverage-target_bed_aligned_reads_in_target_region_pct`
\|\|	DRAGEN: Coverage	Reads on target WGS	Number of uniquely mapped reads to genome relative to the number of uniquely mapped reads to the genome.	`dragen_coverage-wgs_aligned_reads_in_genome_pct`
\|\|	DRAGEN: Coverage	Bases on target BED	Number (millions) of uniquely mapped bases to target region relative to the number of uniquely mapped bases to the genome.	`dragen_coverage-target_bed_aligned_bases_in_target_region_pct`
\|\|	DRAGEN: Coverage	Bases on target WGS	Number (millions) of uniquely mapped bases to genome relative to the number of uniquely mapped bases to the genome.	`dragen_coverage-wgs_aligned_bases_in_genome_pct`
\|\|	DRAGEN: Coverage	Depth BED	Coverage depth over target region: number of uniquely mapped bases to target region divided by the number of sites in target region.	`dragen_coverage-target_bed_average_alignment_coverage_over_target_region`
\|\|	DRAGEN: Coverage	Depth WGS	Coverage depth over genome: number of uniquely mapped bases to genome divided by the number of sites in genome.	`dragen_coverage-wgs_average_alignment_coverage_over_genome`
\|\|	DRAGEN: Coverage	Uniformity(>0.2×mean) BED	Percentage of sites with coverage greater than 20.0% of the mean coverage in target region. Demonstrates the uniformity of coverage, the higher the better.	`dragen_coverage-target_bed_uniformity_of_coverage_pct_0_2_mean_over_target_region`
\|\|	DRAGEN: Coverage	Uniformity(>0.2×mean) WGS	Percentage of sites with coverage greater than 20% of the mean coverage in genome. Demonstrates the uniformity of coverage, the higher the better.	`dragen_coverage-wgs_uniformity_of_coverage_pct_0_2_mean_over_genome`
\|\|	DRAGEN: Coverage	Uniformity(>0.4×mean) BED	Percentage of sites with coverage greater than 40.0% of the mean coverage in target region.	`dragen_coverage-target_bed_uniformity_of_coverage_pct_0_4_mean_over_target_region`
\|\|	DRAGEN: Coverage	Uniformity(>0.4×mean) WGS	Percentage of sites with coverage greater than 40.0% of the mean coverage in genome.	`dragen_coverage-wgs_uniformity_of_coverage_pct_0_4_mean_over_genome`
\|\|	DRAGEN: Coverage	Med aut cov BED	Median alignment coverage over the autosomal loci in target region. If there is no autosome in the reference genome or the target region does not intersect autosomes, this metric shows as NA.	`dragen_coverage-target_bed_median_autosomal_coverage_over_target_region`
\|\|	DRAGEN: Coverage	Med aut cov WGS	Median alignment coverage over the autosomal loci in genome. If there is no autosome in the reference genome or the genome does not intersect autosomes, this metric shows as NA.	`dragen_coverage-wgs_median_autosomal_coverage_over_genome`
\|\|	DRAGEN: Coverage	≥1500x BED	Percentage of sites in target region with at least 1500x coverage.	`dragen_coverage-target_bed_pct_of_target_region_with_coverage_1500x_inf`
\|\|	DRAGEN: Coverage	≥1000x BED	Percentage of sites in target region with at least 1000x coverage.	`dragen_coverage-target_bed_pct_of_target_region_with_coverage_1000x_inf`
\|\|	DRAGEN: Coverage	≥500x BED	Percentage of sites in target region with at least 500x coverage.	`dragen_coverage-target_bed_pct_of_target_region_with_coverage_500x_inf`
\|\|	DRAGEN: Coverage	≥100x BED	Percentage of sites in target region with at least 100x coverage.	`dragen_coverage-target_bed_pct_of_target_region_with_coverage_100x_inf`
\|\|	DRAGEN: Coverage	≥50x BED	Percentage of sites in target region with at least 50x coverage.	`dragen_coverage-target_bed_pct_of_target_region_with_coverage_50x_inf`
\|\|	DRAGEN: Coverage	≥20x BED	Percentage of sites in target region with at least 20x coverage.	`dragen_coverage-target_bed_pct_of_target_region_with_coverage_20x_inf`
\|\|	DRAGEN: Coverage	≥15x BED	Percentage of sites in target region with at least 15x coverage.	`dragen_coverage-target_bed_pct_of_target_region_with_coverage_15x_inf`
\|\|	DRAGEN: Coverage	≥10x BED	Percentage of sites in target region with at least 10x coverage.	`dragen_coverage-target_bed_pct_of_target_region_with_coverage_10x_inf`
\|\|	DRAGEN: Coverage	≥3x BED	Percentage of sites in target region with at least 3x coverage.	`dragen_coverage-target_bed_pct_of_target_region_with_coverage_3x_inf`
\|\|	DRAGEN: Coverage	≥1x BED	Percentage of sites in target region with at least 1x coverage.	`dragen_coverage-target_bed_pct_of_target_region_with_coverage_1x_inf`
\|\|	DRAGEN: Coverage	≥0x BED	Percentage of sites in target region with any coverage.	`dragen_coverage-target_bed_pct_of_target_region_with_coverage_0x_inf`
\|\|	DRAGEN: Coverage	≥1500x WGS	Percentage of sites in genome with at least 1500x coverage.	`dragen_coverage-wgs_pct_of_genome_with_coverage_1500x_inf`
\|\|	DRAGEN: Coverage	≥1000x WGS	Percentage of sites in genome with at least 1000x coverage.	`dragen_coverage-wgs_pct_of_genome_with_coverage_1000x_inf`
\|\|	DRAGEN: Coverage	≥500x WGS	Percentage of sites in genome with at least 500x coverage.	`dragen_coverage-wgs_pct_of_genome_with_coverage_500x_inf`
\|\|	DRAGEN: Coverage	≥100x WGS	Percentage of sites in genome with at least 100x coverage.	`dragen_coverage-wgs_pct_of_genome_with_coverage_100x_inf`
\|\|	DRAGEN: Coverage	≥50x WGS	Percentage of sites in genome with at least 50x coverage.	`dragen_coverage-wgs_pct_of_genome_with_coverage_50x_inf`
\|\|	DRAGEN: Coverage	≥20x WGS	Percentage of sites in genome with at least 20x coverage.	`dragen_coverage-wgs_pct_of_genome_with_coverage_20x_inf`
\|\|	DRAGEN: Coverage	≥15x WGS	Percentage of sites in genome with at least 15x coverage.	`dragen_coverage-wgs_pct_of_genome_with_coverage_15x_inf`
\|\|	DRAGEN: Coverage	≥10x WGS	Percentage of sites in genome with at least 10x coverage.	`dragen_coverage-wgs_pct_of_genome_with_coverage_10x_inf`
\|\|	DRAGEN: Coverage	≥3x WGS	Percentage of sites in genome with at least 3x coverage.	`dragen_coverage-wgs_pct_of_genome_with_coverage_3x_inf`
\|\|	DRAGEN: Coverage	≥1x WGS	Percentage of sites in genome with at least 1x coverage.	`dragen_coverage-wgs_pct_of_genome_with_coverage_1x_inf`
\|\|	DRAGEN: Coverage	≥0x WGS	Percentage of sites in genome with any coverage.	`dragen_coverage-wgs_pct_of_genome_with_coverage_0x_inf`
\|\|	DRAGEN-FastQC: FastQC	% GC	Average % GC Content	`dragen_fastqc_fastqc-avg_gc_content_percent`

DRAGEN

Illumina Bio-IT Platform that uses FPGA for secondary analysis of sequencing data.https://www.illumina.com/products/by-type/informatics-products/dragen-bio-it-platform.html

Mapping metrics

Mapping metrics, similar to the metrics computed by the samtools-stats command. Shown on per read group level. To see per-sample level metrics, refer to the general stats table.

Showing ¹⁶/₁₆ rows and ¹³/₇₀ columns.

Sample Name	Input reads	M Input reads	Paired	M Paired	Single	M Single	QC-fail	M QC-fail	Map	M Map	Map R1	M Map R1	Map R2	M Map R2	Unmap	M Unmap	MQ⩾40	M MQ⩾40	Dup	M Dup	Uniq	Self & mate map	M Self & mate map	Prop pair	M Prop pair	Discord	M Discord	Singleton	M Singleton	Diff chrom	M Diff chrom	Diff chr, MQ⩾10	M Diff chr, MQ⩾10	Reads with indel R1	M Reads with indel R1	Reads with indel R2	M Reads with indel R2	Read len	Avg IS	Med IS	IS std	Mb Input bases	Mb Input bases R1	Mb Input bases R2	Mapped bases R1	Mb Mapped bases R1	Mapped bases R2	Mb Mapped bases R2	Soft-clip bases R1	Mb Soft-clip bases R1	Soft-clip bases R2	MM bases R1	Mb MM bases R1	MM bases R2	MM bases R1 excl indels	Mb MM bases R1 excl indels	MM bases R2 excl indels	Q30	Mb Q30	Q30 R1	Mb Q30 R1	Q30 R2	Mb Q30 R2	Q30 excl dup & clipped	Mb Q30 excl dup & clipped	M Alignments	Sec'ry	M Sec'ry	Suppl'ry	M Suppl'ry
Alp13-1-20 \| Alp13-1-20	100.0%	0.1M	100.0%	0.1M	0.0%	0.0M	0.00%	0.00M	97.5%	0.1M	98.0%	0.1M	96.9%	0.1M	2.5%	0.0M	97.4%	0.1M	0.0%	0.0M	100.0%	96.9%	0.1M	93.1%	0.1M	3.77%	0.01M	0.58%	0.00M	0.10%	0.00M	0.07%	0.00M	2.9%	0.0M	4.3%	0.0M	147.6	226.8	217	106.7	20.2Mb	10.1Mb	10.1Mb	49.7%	10.0Mb	49.1%	9.9Mb	0.6%	0.1Mb	0.8%	0.2%	0.0Mb	0.3%	0.2%	0.0Mb	0.2%	95.9%	19.4Mb	97.5%	9.8Mb	94.3%	9.5Mb	95.3%	19.3Mb	0.1M	0.00%	0.00M	0.13%	0.00M
Alp13-1-100 \| Alp13-1-100	100.0%	0.1M	100.0%	0.1M	0.0%	0.0M	0.00%	0.00M	98.7%	0.1M	99.3%	0.1M	98.0%	0.1M	1.3%	0.0M	98.6%	0.1M	0.0%	0.0M	100.0%	98.0%	0.1M	95.2%	0.1M	2.78%	0.00M	0.68%	0.00M	0.09%	0.00M	0.06%	0.00M	2.9%	0.0M	4.3%	0.0M	149.4	229.4	217	47.9	19.0Mb	9.5Mb	9.5Mb	49.9%	9.5Mb	49.2%	9.4Mb	0.5%	0.0Mb	0.8%	0.2%	0.0Mb	0.3%	0.2%	0.0Mb	0.2%	96.5%	18.4Mb	97.8%	9.3Mb	95.3%	9.1Mb	96.0%	18.3Mb	0.1M	0.00%	0.00M	0.15%	0.00M
Alp22-1-20 \| Alp22-1-20	100.0%	0.1M	100.0%	0.1M	0.0%	0.0M	0.00%	0.00M	99.0%	0.1M	99.7%	0.1M	98.4%	0.1M	0.9%	0.0M	98.9%	0.1M	0.0%	0.0M	100.0%	98.4%	0.1M	97.7%	0.1M	0.69%	0.00M	0.65%	0.00M	0.09%	0.00M	0.07%	0.00M	2.9%	0.0M	3.2%	0.0M	149.6	223.1	222	112.2	18.7Mb	9.3Mb	9.3Mb	49.9%	9.3Mb	49.3%	9.2Mb	0.7%	0.1Mb	0.7%	0.1%	0.0Mb	0.5%	0.1%	0.0Mb	0.4%	94.8%	17.7Mb	97.7%	9.1Mb	92.0%	8.6Mb	94.3%	17.6Mb	0.1M	0.00%	0.00M	0.14%	0.00M
Alp22-1-100 \| Alp22-1-100	100.0%	0.1M	100.0%	0.1M	0.0%	0.0M	0.00%	0.00M	99.1%	0.1M	99.7%	0.1M	98.5%	0.1M	0.9%	0.0M	98.9%	0.1M	0.0%	0.0M	100.0%	98.4%	0.1M	94.9%	0.1M	3.53%	0.00M	0.66%	0.00M	0.07%	0.00M	0.06%	0.00M	2.9%	0.0M	3.2%	0.0M	149.8	225.7	222	137.5	20.6Mb	10.3Mb	10.3Mb	49.9%	10.3Mb	49.3%	10.2Mb	0.7%	0.1Mb	0.6%	0.2%	0.0Mb	0.3%	0.1%	0.0Mb	0.3%	96.0%	19.8Mb	97.8%	10.1Mb	94.3%	9.7Mb	95.5%	19.7Mb	0.1M	0.00%	0.00M	0.13%	0.00M
Alp32-1-20 \| Alp32-1-20	100.0%	0.1M	100.0%	0.1M	0.0%	0.0M	0.00%	0.00M	99.3%	0.1M	99.8%	0.1M	98.8%	0.1M	0.7%	0.0M	99.2%	0.1M	0.0%	0.0M	100.0%	98.8%	0.1M	98.2%	0.1M	0.62%	0.00M	0.52%	0.00M	0.10%	0.00M	0.08%	0.00M	4.8%	0.0M	7.8%	0.0M	149.9	237.0	244	48.5	19.9Mb	9.9Mb	9.9Mb	49.9%	9.9Mb	49.4%	9.8Mb	0.6%	0.1Mb	2.7%	0.3%	0.0Mb	0.9%	0.1%	0.0Mb	0.7%	93.1%	18.5Mb	97.6%	9.7Mb	88.6%	8.8Mb	92.4%	18.4Mb	0.1M	0.00%	0.00M	0.03%	0.00M
Alp32-1-100 \| Alp32-1-100	100.0%	0.1M	100.0%	0.1M	0.0%	0.0M	0.00%	0.00M	99.2%	0.1M	99.7%	0.1M	98.6%	0.1M	0.8%	0.0M	99.0%	0.1M	0.0%	0.0M	100.0%	98.6%	0.1M	97.9%	0.1M	0.73%	0.00M	0.53%	0.00M	0.10%	0.00M	0.08%	0.00M	4.7%	0.0M	8.6%	0.0M	149.6	238.2	244	106.7	17.7Mb	8.9Mb	8.9Mb	49.9%	8.8Mb	49.4%	8.8Mb	0.6%	0.0Mb	3.2%	0.3%	0.0Mb	0.9%	0.1%	0.0Mb	0.8%	93.0%	16.5Mb	97.6%	8.6Mb	88.5%	7.9Mb	92.3%	16.4Mb	0.1M	0.00%	0.00M	0.04%	0.00M
Alp42-1-20 \| Alp42-1-20	100.0%	0.1M	100.0%	0.1M	0.0%	0.0M	0.00%	0.00M	98.2%	0.1M	98.9%	0.1M	97.5%	0.1M	1.8%	0.0M	98.1%	0.1M	0.0%	0.0M	100.0%	97.5%	0.1M	92.1%	0.1M	5.35%	0.01M	0.74%	0.00M	0.10%	0.00M	0.08%	0.00M	2.8%	0.0M	2.5%	0.0M	148.8	239.7	235	153.2	20.1Mb	10.1Mb	10.0Mb	49.8%	10.0Mb	49.0%	9.8Mb	0.6%	0.1Mb	0.7%	0.1%	0.0Mb	0.3%	0.1%	0.0Mb	0.3%	94.9%	19.1Mb	97.2%	9.8Mb	92.7%	9.3Mb	94.4%	19.0Mb	0.1M	0.00%	0.00M	0.03%	0.00M
Alp42-1-100 \| Alp42-1-100	100.0%	0.1M	100.0%	0.1M	0.0%	0.0M	0.00%	0.00M	98.3%	0.1M	99.2%	0.1M	97.5%	0.1M	1.7%	0.0M	98.2%	0.1M	0.0%	0.0M	100.0%	97.5%	0.1M	92.0%	0.1M	5.42%	0.01M	0.85%	0.00M	0.12%	0.00M	0.10%	0.00M	2.8%	0.0M	2.4%	0.0M	149.1	239.6	235	87.0	18.7Mb	9.4Mb	9.3Mb	49.9%	9.3Mb	48.9%	9.1Mb	0.6%	0.1Mb	0.6%	0.1%	0.0Mb	0.2%	0.1%	0.0Mb	0.2%	95.7%	17.9Mb	97.2%	9.1Mb	94.1%	8.8Mb	95.2%	17.8Mb	0.1M	0.00%	0.00M	0.03%	0.00M
Alp52-1-20 \| Alp52-1-20	100.0%	0.1M	100.0%	0.1M	0.0%	0.0M	0.00%	0.00M	99.2%	0.1M	99.8%	0.1M	98.7%	0.1M	0.8%	0.0M	99.1%	0.1M	0.0%	0.0M	100.0%	98.6%	0.1M	96.2%	0.1M	2.45%	0.00M	0.57%	0.00M	0.08%	0.00M	0.06%	0.00M	3.8%	0.0M	4.0%	0.0M	150.0	222.8	214	42.1	20.2Mb	10.1Mb	10.1Mb	49.9%	10.1Mb	49.3%	10.0Mb	0.5%	0.0Mb	1.0%	0.2%	0.0Mb	0.5%	0.2%	0.0Mb	0.4%	95.7%	19.3Mb	97.6%	9.9Mb	93.7%	9.5Mb	95.2%	19.2Mb	0.1M	0.00%	0.00M	0.03%	0.00M
Alp52-1-100 \| Alp52-1-100	100.0%	0.1M	100.0%	0.1M	0.0%	0.0M	0.00%	0.00M	99.2%	0.1M	99.8%	0.1M	98.5%	0.1M	0.8%	0.0M	99.1%	0.1M	0.0%	0.0M	100.0%	98.5%	0.1M	95.4%	0.1M	3.11%	0.00M	0.64%	0.00M	0.08%	0.00M	0.06%	0.00M	4.2%	0.0M	4.1%	0.0M	150.1	224.1	214	39.2	18.0Mb	9.0Mb	9.0Mb	50.0%	9.0Mb	49.3%	8.9Mb	0.4%	0.0Mb	1.0%	0.2%	0.0Mb	0.4%	0.2%	0.0Mb	0.4%	96.2%	17.4Mb	97.7%	8.8Mb	94.8%	8.5Mb	95.8%	17.3Mb	0.1M	0.00%	0.00M	0.03%	0.00M
Alp62-1-20 \| Alp62-1-20	100.0%	0.2M	100.0%	0.2M	0.0%	0.0M	0.00%	0.00M	98.8%	0.2M	99.6%	0.1M	98.1%	0.1M	1.1%	0.0M	98.3%	0.2M	0.0%	0.0M	100.0%	98.1%	0.2M	91.9%	0.1M	6.21%	0.01M	0.75%	0.00M	0.14%	0.00M	0.10%	0.00M	5.7%	0.0M	3.6%	0.0M	149.5	228.0	220	105.3	23.9Mb	11.9Mb	11.9Mb	49.9%	11.9Mb	49.1%	11.7Mb	0.7%	0.1Mb	1.2%	0.2%	0.0Mb	0.3%	0.2%	0.0Mb	0.3%	95.8%	22.9Mb	97.6%	11.7Mb	93.9%	11.2Mb	95.0%	22.7Mb	0.2M	0.00%	0.00M	0.22%	0.00M
Alp62-1-100 \| Alp62-1-100	100.0%	0.2M	100.0%	0.2M	0.0%	0.0M	0.00%	0.00M	98.8%	0.2M	99.6%	0.1M	97.9%	0.1M	1.2%	0.0M	98.3%	0.2M	0.0%	0.0M	100.0%	97.9%	0.2M	94.0%	0.1M	3.87%	0.01M	0.86%	0.00M	0.16%	0.00M	0.13%	0.00M	6.6%	0.0M	3.9%	0.0M	149.5	229.9	223	125.2	23.1Mb	11.6Mb	11.5Mb	49.9%	11.5Mb	49.0%	11.3Mb	0.7%	0.1Mb	1.2%	0.2%	0.0Mb	0.3%	0.2%	0.0Mb	0.2%	96.2%	22.2Mb	97.7%	11.3Mb	94.8%	10.9Mb	95.5%	22.0Mb	0.2M	0.00%	0.00M	0.21%	0.00M
AlpP2-NG011977-1-20 \| AlpP2-NG011977-1-20	100.0%	0.1M	100.0%	0.1M	0.0%	0.0M	0.00%	0.00M	94.2%	0.1M	95.0%	0.1M	93.4%	0.1M	5.8%	0.0M	94.1%	0.1M	0.0%	0.0M	100.0%	93.4%	0.1M	93.2%	0.1M	0.22%	0.00M	0.81%	0.00M	0.11%	0.00M	0.08%	0.00M	3.5%	0.0M	4.4%	0.0M	145.2	241.9	245	83.0	19.3Mb	9.7Mb	9.7Mb	49.3%	9.5Mb	48.5%	9.4Mb	0.3%	0.0Mb	0.2%	0.1%	0.0Mb	0.2%	0.1%	0.0Mb	0.2%	94.8%	18.3Mb	96.7%	9.4Mb	92.9%	9.0Mb	94.6%	18.3Mb	0.1M	0.00%	0.00M	0.01%	0.00M
AlpP2-NG011977-1-100 \| AlpP2-NG011977-1-100	100.0%	0.1M	100.0%	0.1M	0.0%	0.0M	0.00%	0.00M	96.5%	0.1M	97.3%	0.1M	95.8%	0.1M	3.5%	0.0M	96.5%	0.1M	0.0%	0.0M	100.0%	95.7%	0.1M	48.0%	0.1M	47.70%	0.06M	0.82%	0.00M	0.09%	0.00M	0.07%	0.00M	3.6%	0.0M	4.5%	0.0M	147.8	256.5	273	103.5	19.2Mb	9.6Mb	9.6Mb	49.6%	9.5Mb	48.8%	9.4Mb	0.3%	0.0Mb	0.2%	0.1%	0.0Mb	0.2%	0.1%	0.0Mb	0.2%	95.7%	18.3Mb	97.3%	9.3Mb	94.1%	9.0Mb	95.5%	18.3Mb	0.1M	0.00%	0.00M	0.00%	0.00M
AlpP3-1-20 \| AlpP3-1-20	100.0%	0.1M	100.0%	0.1M	0.0%	0.0M	0.00%	0.00M	94.9%	0.1M	95.5%	0.1M	94.3%	0.1M	5.1%	0.0M	94.7%	0.1M	0.0%	0.0M	100.0%	94.3%	0.1M	93.0%	0.1M	1.27%	0.00M	0.62%	0.00M	0.14%	0.00M	0.09%	0.00M	2.8%	0.0M	4.0%	0.0M	142.8	222.3	222	65.0	19.4Mb	9.7Mb	9.7Mb	49.3%	9.6Mb	48.8%	9.5Mb	0.6%	0.1Mb	0.7%	0.2%	0.0Mb	0.4%	0.2%	0.0Mb	0.4%	95.3%	18.5Mb	96.9%	9.4Mb	93.7%	9.1Mb	94.8%	18.4Mb	0.1M	0.00%	0.00M	0.11%	0.00M
AlpP3-1-100 \| AlpP3-1-100	100.0%	0.1M	100.0%	0.1M	0.0%	0.0M	0.00%	0.00M	97.6%	0.1M	98.3%	0.1M	96.9%	0.1M	2.4%	0.0M	97.5%	0.1M	0.0%	0.0M	100.0%	96.9%	0.1M	96.1%	0.1M	0.75%	0.00M	0.71%	0.00M	0.12%	0.00M	0.08%	0.00M	2.9%	0.0M	4.1%	0.0M	147.2	226.3	222	91.5	21.8Mb	10.9Mb	10.9Mb	49.7%	10.8Mb	49.1%	10.7Mb	0.4%	0.0Mb	0.6%	0.2%	0.0Mb	0.4%	0.2%	0.0Mb	0.3%	96.4%	21.0Mb	97.6%	10.6Mb	95.2%	10.4Mb	96.1%	21.0Mb	0.1M	0.00%	0.00M	0.17%	0.00M

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: dragen-mapping-metrics-table_table

Sort	Column	Description	ID	Scale
\|\|	Input reads	Total number of reads in this RG	`mapping-Total_reads_in_RG_pct`
\|\|	M Input reads	Total number of reads in this RG, millions	`mapping-Total_reads_in_RG`	read_count
\|\|	Paired	% of reads with a mate sequenced	`mapping-Reads_with_mate_sequenced_pct`
\|\|	M Paired	Number of reads with a mate sequenced, millions	`mapping-Reads_with_mate_sequenced`	read_count
\|\|	Single	% of reads without a mate sequenced	`mapping-Reads_without_mate_sequenced_pct`
\|\|	M Single	Number of reads without a mate sequenced, millions	`mapping-Reads_without_mate_sequenced`	read_count
\|\|	QC-fail	% of reads not passing platform/vendor quality checks (SAM flag 0x200)	`mapping-QC_failed_reads_pct`
\|\|	M QC-fail	Number of reads not passing platform/vendor quality checks (SAM flag 0x200), millions	`mapping-QC_failed_reads`	read_count
\|\|	Map	% of mapped reads	`mapping-Mapped_reads_pct`
\|\|	M Map	Number of mapped reads, millions	`mapping-Mapped_reads`	read_count
\|\|	Map R1	% of mapped reads R1	`mapping-Mapped_reads_R1_pct`
\|\|	M Map R1	Number of mapped reads R1, millions	`mapping-Mapped_reads_R1`	read_count
\|\|	Map R2	% of mapped reads R2	`mapping-Mapped_reads_R2_pct`
\|\|	M Map R2	Number of mapped reads R2, millions	`mapping-Mapped_reads_R2`	read_count
\|\|	Unmap	% of unmapped reads	`mapping-Unmapped_reads_pct`
\|\|	M Unmap	Number of unmapped reads, millions	`mapping-Unmapped_reads`	read_count
\|\|	MQ⩾40	% of reads with MAPQ [40:inf)	`mapping-Reads_with_MAPQ_40_inf_pct`
\|\|	M MQ⩾40	Number of reads with MAPQ [40:inf), millions	`mapping-Reads_with_MAPQ_40_inf`	read_count
\|\|	Dup	% of duplicate marked reads as a result of the --enable-duplicatemarking option being used	`mapping-Number_of_duplicate_marked_reads_pct`
\|\|	M Dup	Number of duplicate marked reads as a result of the --enable-duplicatemarking option being used, millions	`mapping-Number_of_duplicate_marked_reads`	read_count
\|\|	Uniq	% of unique reads (all reads minus duplicate marked reads)	`mapping-Number_of_unique_reads_excl_duplicate_marked_reads_pct`
\|\|	Self & mate map	% of reads mapped in pairs (itself & mate mapped)	`mapping-Paired_reads_itself_mate_mapped_pct`
\|\|	M Self & mate map	Number of reads mapped in pairs (itself & mate mapped), millions	`mapping-Paired_reads_itself_mate_mapped`	read_count
\|\|	Prop pair	% of properly paired reads (both reads in pair are mapped and fall within an acceptable range from each other based on the estimated insert length distribution). Duplicate and low quality reads are not excluded, i.e. the percentage is calculated relative to the total number of reads.	`mapping-Properly_paired_reads_pct`
\|\|	M Prop pair	Number of properly paired reads, millions (both reads in pair are mapped and fall within an acceptable range from each other based on the estimated insert length distribution). Duplicate and low quality reads are not excluded, i.e. the percentage is calculated relative to the total number of reads.	`mapping-Properly_paired_reads`	read_count
\|\|	Discord	% of discordant reads: paired reads minus properly paired reads	`mapping-Not_properly_paired_reads_discordant_pct`
\|\|	M Discord	Number of discordant reads: paired reads minus properly paired reads , millions	`mapping-Not_properly_paired_reads_discordant`	read_count
\|\|	Singleton	% of singleton reads: itself mapped; mate unmapped	`mapping-Singleton_reads_itself_mapped_mate_unmapped_pct`
\|\|	M Singleton	Number of singleton reads: itself mapped; mate unmapped, millions	`mapping-Singleton_reads_itself_mapped_mate_unmapped`	read_count
\|\|	Diff chrom	% of paired reads with a mate mapped to a different chromosome	`mapping-Paired_reads_mapped_to_different_chromosomes_pct`
\|\|	M Diff chrom	Number of paired reads with a mate mapped to a different chromosome, millions	`mapping-Paired_reads_mapped_to_different_chromosomes`	read_count
\|\|	Diff chr, MQ⩾10	% of paired reads, mapped with MAPQ>=10 and with a mate mapped to a different chromosome	`mapping-Paired_reads_mapped_to_different_chromosomes_MAPQ_10_pct`
\|\|	M Diff chr, MQ⩾10	Number of paired reads, mapped with MAPQ>=10 and with a mate mapped to a different chromosome, millions	`mapping-Paired_reads_mapped_to_different_chromosomes_MAPQ_10`	read_count
\|\|	Reads with indel R1	% of R1 reads containing at least 1 indel	`mapping-Reads_with_indel_R1_pct`
\|\|	M Reads with indel R1	Number of R1 reads containing at least 1 indel, millions	`mapping-Reads_with_indel_R1`	read_count
\|\|	Reads with indel R2	% of R2 reads containing at least 1 indel	`mapping-Reads_with_indel_R2_pct`
\|\|	M Reads with indel R2	Number of R2 reads containing at least 1 indel, millions	`mapping-Reads_with_indel_R2`	read_count
\|\|	Read len	Estimated read length. Total number of input bases divided by the number of reads	`mapping-Estimated_read_length`
\|\|	Avg IS	Mean insert size	`mapping-Insert_length_mean`
\|\|	Med IS	Median insert size	`mapping-Insert_length_median`
\|\|	IS std	Standard deviation of insert size deviation	`mapping-Insert_length_standard_deviation`
\|\|	Mb Input bases	Total number of bases sequenced, millions	`mapping-Total_bases`	base_count
\|\|	Mb Input bases R1	Total number of bases sequenced on R1 reads, millions	`mapping-Total_bases_R1`	base_count
\|\|	Mb Input bases R2	Total number of bases sequenced on R2 reads, millions	`mapping-Total_bases_R2`	base_count
\|\|	Mapped bases R1	% of mapped bases on R1 reads	`mapping-Mapped_bases_R1_pct`
\|\|	Mb Mapped bases R1	Number of mapped bases on R1 reads, millions	`mapping-Mapped_bases_R1`	base_count
\|\|	Mapped bases R2	% of mapped bases on R2 reads	`mapping-Mapped_bases_R2_pct`
\|\|	Mb Mapped bases R2	Number of mapped bases on R2 reads, millions	`mapping-Mapped_bases_R2`	base_count
\|\|	Soft-clip bases R1	% of soft-clipped bases on R1 reads	`mapping-Soft_clipped_bases_R1_pct`
\|\|	Mb Soft-clip bases R1	Number of soft-clipped bases on R1 reads, millions	`mapping-Soft_clipped_bases_R1`	base_count
\|\|	Soft-clip bases R2	% of soft-clipped bases on R2 reads	`mapping-Soft_clipped_bases_R2_pct`
\|\|	MM bases R1	% of mismatched bases on R1, which is the sum of SNP count and indel lengths. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`mapping-Mismatched_bases_R1_pct`
\|\|	Mb MM bases R1	Number of mismatched bases on R1, millions, which is the sum of SNP count and indel lengths. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`mapping-Mismatched_bases_R1`	base_count
\|\|	MM bases R2	% of mismatched bases on R2, which is the sum of SNP count and indel lengths. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`mapping-Mismatched_bases_R2_pct`
\|\|	MM bases R1 excl indels	% of mismatched bases on R1. The indels lengts are ignored. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`mapping-Mismatched_bases_R1_excl_indels_pct`
\|\|	Mb MM bases R1 excl indels	Number of mismatched bases on R1, millions. The indels lengts are ignored. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`mapping-Mismatched_bases_R1_excl_indels`	base_count
\|\|	MM bases R2 excl indels	% of mismatched bases on R2. The indels lengts are ignored. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`mapping-Mismatched_bases_R2_excl_indels_pct`
\|\|	Q30	% of raw bases with BQ >= 30	`mapping-Q30_bases_pct`
\|\|	Mb Q30	Number of raw bases with BQ >= 30, millions	`mapping-Q30_bases`	base_count
\|\|	Q30 R1	% of raw bases on R1 reads with BQ >= 30	`mapping-Q30_bases_R1_pct`
\|\|	Mb Q30 R1	Number of raw bases on R1 reads with BQ >= 30, millions	`mapping-Q30_bases_R1`	base_count
\|\|	Q30 R2	% of raw bases on R2 reads with BQ >= 30	`mapping-Q30_bases_R2_pct`
\|\|	Mb Q30 R2	Number of raw bases on R2 reads with BQ >= 30, millions	`mapping-Q30_bases_R2`	base_count
\|\|	Q30 excl dup & clipped	% of non-clipped bases with BQ >= 30 on non-duplicate reads	`mapping-Q30_bases_excl_dups_clipped_bases_pct`
\|\|	Mb Q30 excl dup & clipped	Number of non-clipped bases with BQ >= 30 on non-duplicate reads, millions	`mapping-Q30_bases_excl_dups_clipped_bases`	base_count
\|\|	M Alignments	Total number of alignments with MQ > 0, millions	`mapping-Total_alignments`	read_count
\|\|	Sec'ry	% of secondary alignments. Secondary alignment occurs when a given read could align reasonably well to more than one place. One of the possible reported alignments is termed "primary" and the others will be marked as "secondary".	`mapping-Secondary_alignments_pct`
\|\|	M Sec'ry	Number of secondary alignments, millions. Secondary alignment occurs when a given read could align reasonably well to more than one place. One of the possible reported alignments is termed "primary" and the others will be marked as "secondary".	`mapping-Secondary_alignments`	read_count
\|\|	Suppl'ry	% of supplementary (chimeric) alignments. A chimeric read is split over multiple loci (possibly due to structural variants). One alignment is referred to as the representative alignment, the other are supplementary	`mapping-Supplementary_chimeric_alignments_pct`
\|\|	M Suppl'ry	Number of supplementary (chimeric) alignments, millions. A chimeric read is split over multiple loci (possibly due to structural variants). One alignment is referred to as the representative alignment, the other are supplementary	`mapping-Supplementary_chimeric_alignments`	read_count

Mapped / paired / duplicated

Distribution of reads based on pairing, duplication and mapping.

Created with MultiQC

Target Bed Coverage Metrics

Coverage metrics over target Bed. All samples are based on the target_bed.

Press the Help button for details.

The following criteria are used when calculating coverage:

Duplicate reads and clipped bases are ignored.
DRAGEN V3.4 - 3.7: Only reads with MAPQ > min MAPQ and bases with BQ > min BQ are considered
DRAGEN V3.8 - 4.1: By default, reads with MAPQ < 1 and bases with BQ < 0 are ignored. You can use the qc-coverage-filters-n option to specify which BQ bases and MAPQ reads to filter out.

Considering only bases usable for variant calling, i.e. excluding:

Clipped bases
Bases in duplicate reads
Reads with MAPQ < min MAPQ (default 20)
Bases with BQ < min BQ (default 10)
Reads with MAPQ = 0 (multimappers)
Overlapping mates are double-counted

Each _coverage_metrics.csv file may have an associated _overall_mean_cov.csv file. The latter contains the 'Average alignment coverage over <source file>' metric. Information about <source file>s can be found in the section's description or in this drop-list below if the produced text is long. If input directory does not contain _overall_mean_cov files, then "No 'coverage bed/target bed/wgs' source file found" is printed.

Showing ¹⁶/₁₆ rows and ⁵/₃₆ columns.

Sample Name	Aln reads	Reads on target	Reads on target	Aln bases	Bases on target	Bases on target	Depth	MT cov	Uniformity(>0.2×mean)	Uniformity(>0.4×mean)	Mean aut cov	Med aut cov	Mean/med autosomal coverage	≥1500x	≥1000x	≥500x	≥100x	≥50x	≥20x	≥15x	≥10x	≥3x	≥1x	≥0x	[1000x:1500x)	[500x:1000x)	[100x:500x)	[50x:100x)	[20x:50x)	[15x:20x)	[10x:15x)	[3x:10x)	[1x:3x)	0x	median chr x coverage (ignore 0x regions) over target region
Alp13-1-20 \| Alp13-1-20	0.1M	0.1M	83.0%	19.8Mb	11.7Mb	59.2%	258.71x	0.00x	8.64%	8.64%	486.88x	3658.50x	0.13x	5.43%	6.85%	8.01%	8.64%	8.64%	8.64%	8.64%	8.64%	9.10%	16.93%	100.00%	1.42%	1.16%	0.63%	0.00%	0.00%	0.00%	0.00%	0.47%	7.82%	83.07%	1.00
Alp13-1-100 \| Alp13-1-100	0.1M	0.1M	81.8%	18.8Mb	10.8Mb	57.7%	238.63x	0.00x	8.64%	8.64%	449.11x	2955.00x	0.15x	5.65%	7.05%	8.12%	8.64%	8.64%	8.64%	8.64%	8.64%	8.95%	14.52%	100.00%	1.40%	1.07%	0.52%	0.00%	0.00%	0.00%	0.00%	0.31%	5.57%	85.48%	1.00
Alp22-1-20 \| Alp22-1-20	0.1M	0.1M	88.4%	18.4Mb	8.0Mb	43.7%	176.93x	0.00x	7.86%	7.86%	332.92x	2024.00x	0.16x	4.46%	5.42%	7.08%	7.86%	7.86%	7.86%	7.86%	7.86%	8.72%	13.74%	100.00%	0.96%	1.66%	0.77%	0.00%	0.00%	0.00%	0.00%	0.87%	5.02%	86.26%	1.00
Alp22-1-100 \| Alp22-1-100	0.1M	0.1M	88.4%	20.3Mb	8.8Mb	43.4%	194.42x	0.00x	7.86%	7.86%	365.86x	2191.00x	0.17x	4.70%	5.64%	7.13%	7.86%	7.86%	7.86%	7.86%	7.95%	8.44%	14.30%	100.00%	0.94%	1.48%	0.73%	0.00%	0.00%	0.00%	0.09%	0.49%	5.86%	85.70%	1.00
Alp32-1-20 \| Alp32-1-20	0.1M	0.1M	80.4%	19.4Mb	8.0Mb	41.3%	176.40x	0.00x	7.33%	7.33%	0.10x	1.00x	0.10x	4.25%	5.16%	6.58%	7.11%	7.33%	7.33%	7.33%	7.33%	7.59%	12.63%	100.00%	0.91%	1.42%	0.53%	0.22%	0.00%	0.00%	0.00%	0.27%	5.04%	87.37%	1510.00
Alp32-1-100 \| Alp32-1-100	0.1M	0.1M	80.5%	17.3Mb	7.1Mb	41.2%	156.76x	0.00x	7.33%	7.33%	0.16x	1.00x	0.16x	3.65%	4.81%	6.20%	7.18%	7.33%	7.33%	7.33%	7.33%	8.05%	13.51%	100.00%	1.16%	1.39%	0.98%	0.15%	0.00%	0.00%	0.00%	0.72%	5.47%	86.49%	1441.00
Alp42-1-20 \| Alp42-1-20	0.1M	0.1M	96.0%	19.7Mb	10.2Mb	51.9%	225.55x	0.00x	5.94%	5.54%	0.13x	1.00x	0.13x	4.15%	4.76%	4.91%	5.54%	5.93%	5.94%	5.94%	5.94%	6.16%	13.01%	100.00%	0.61%	0.15%	0.63%	0.39%	0.00%	0.00%	0.00%	0.22%	6.85%	86.99%	1596.00
Alp42-1-100 \| Alp42-1-100	0.1M	0.1M	96.1%	18.3Mb	9.6Mb	52.1%	210.69x	0.00x	5.94%	5.54%	0.16x	1.00x	0.16x	3.59%	4.63%	4.76%	5.54%	5.92%	5.94%	5.94%	5.94%	6.33%	14.07%	100.00%	1.04%	0.13%	0.78%	0.38%	0.02%	0.00%	0.00%	0.40%	7.73%	85.93%	1429.00
Alp52-1-20 \| Alp52-1-20	0.1M	0.1M	78.5%	19.9Mb	7.6Mb	38.1%	166.93x	0.00x	14.00%	13.43%	224.68x	1053.00x	0.21x	3.12%	4.06%	7.72%	12.94%	13.95%	14.00%	14.00%	14.07%	14.13%	15.73%	100.00%	0.94%	3.66%	5.21%	1.01%	0.06%	0.00%	0.06%	0.07%	1.60%	84.27%	379.00
Alp52-1-100 \| Alp52-1-100	0.1M	0.1M	78.2%	17.8Mb	6.8Mb	38.1%	149.07x	0.00x	14.00%	13.43%	201.43x	945.00x	0.21x	2.91%	3.64%	7.19%	12.65%	13.70%	14.00%	14.00%	14.12%	14.13%	19.00%	100.00%	0.73%	3.55%	5.47%	1.04%	0.31%	0.00%	0.11%	0.02%	4.87%	81.00%	293.00
Alp62-1-20 \| Alp62-1-20	0.2M	0.1M	82.7%	23.3Mb	12.4Mb	53.2%	273.65x	0.00x	10.17%	10.17%	515.04x	3480.00x	0.15x	5.99%	6.94%	8.29%	10.17%	10.22%	10.34%	10.34%	10.34%	10.78%	16.34%	100.00%	0.95%	1.35%	1.87%	0.06%	0.12%	0.00%	0.00%	0.44%	5.57%	83.66%	1.00
Alp62-1-100 \| Alp62-1-100	0.2M	0.1M	82.3%	22.6Mb	12.0Mb	53.2%	264.53x	0.00x	10.17%	10.17%	497.83x	3553.00x	0.14x	5.90%	7.18%	9.00%	10.17%	10.17%	10.23%	10.34%	10.34%	11.46%	17.63%	100.00%	1.28%	1.82%	1.17%	0.00%	0.06%	0.11%	0.00%	1.12%	6.17%	82.37%	1.00
AlpP2-NG011977-1-20 \| AlpP2-NG011977-1-20	0.1M	0.1M	77.8%	18.8Mb	8.9Mb	47.5%	197.19x	0.00x	2.23%	2.23%	0.11x	1.00x	0.11x	2.12%	2.12%	2.16%	2.23%	2.23%	2.23%	2.23%	2.23%	2.70%	7.58%	100.00%	0.00%	0.05%	0.06%	0.00%	0.00%	0.00%	0.00%	0.48%	4.88%	92.42%	6654.00
AlpP2-NG011977-1-100 \| AlpP2-NG011977-1-100	0.1M	0.1M	79.1%	18.8Mb	9.3Mb	49.4%	204.94x	0.00x	2.23%	2.23%	0.10x	1.00x	0.10x	1.97%	2.12%	2.12%	2.22%	2.23%	2.23%	2.23%	2.23%	2.40%	8.83%	100.00%	0.15%	0.00%	0.10%	0.01%	0.00%	0.00%	0.00%	0.18%	6.43%	91.17%	2.00
AlpP3-1-20 \| AlpP3-1-20	0.1M	0.1M	72.5%	18.9Mb	4.2Mb	22.2%	92.50x	0.00x	1.55%	1.55%	174.00x	1.00x	174.00x	1.55%	1.55%	1.55%	1.55%	1.55%	1.55%	1.55%	1.55%	2.13%	9.58%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.58%	7.45%	90.42%	1.00
AlpP3-1-100 \| AlpP3-1-100	0.1M	0.1M	72.3%	21.4Mb	4.7Mb	22.1%	104.34x	0.00x	1.55%	1.55%	196.34x	2.00x	98.17x	1.55%	1.55%	1.55%	1.55%	1.55%	1.55%	1.55%	1.55%	2.48%	10.53%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.92%	8.05%	89.47%	1.00

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: dragen-cov-metrics-own-section-target-bed-table_table

Sort	Group	Column	Description	ID	Scale
\|\|	Coverage	Aln reads	Total number (millions) of aligned reads.	`coverage-target_bed_aligned_reads`	read_count
\|\|	Coverage	Reads on target	Number (millions) of uniquely mapped reads to target region. DRAGEN V3.4 - V3.8: When region is the target BED, this metric is equivalent to and replaces Capture Specificity based on target region. DRAGEN V3.9 - V4.1: Only reads with MAPQ >= 1 are included. Secondary and supplementary alignments are ignored.	`coverage-target_bed_aligned_reads_in_target_region`	read_count
\|\|	Coverage	Reads on target	Number of uniquely mapped reads to target region relative to the number of uniquely mapped reads to the genome.	`coverage-target_bed_aligned_reads_in_target_region_pct`
\|\|	Coverage	Aln bases	Total number (millions) of aligned bases.	`coverage-target_bed_aligned_bases`	base_count
\|\|	Coverage	Bases on target	Number (millions) of uniquely mapped bases to target region.	`coverage-target_bed_aligned_bases_in_target_region`	base_count
\|\|	Coverage	Bases on target	Number (millions) of uniquely mapped bases to target region relative to the number of uniquely mapped bases to the genome.	`coverage-target_bed_aligned_bases_in_target_region_pct`
\|\|	Coverage	Depth	Coverage depth over target region: number of uniquely mapped bases to target region divided by the number of sites in target region.	`coverage-target_bed_average_alignment_coverage_over_target_region`
\|\|	Coverage	MT cov	Total number of bases that aligned to the intersection of the mitochondrial chromosome with target region divided by the total number of loci in the intersection of the mitochondrial chromosome with target region. If there is no mitochondrial chromosome in the reference genome or the target region does not intersect mitochondrial chromosome, this metric shows as NA.	`coverage-target_bed_average_mitochondrial_coverage_over_target_region`
\|\|	Coverage	Uniformity(>0.2×mean)	Percentage of sites with coverage greater than 20.0% of the mean coverage in target region. Demonstrates the uniformity of coverage, the higher the better.	`coverage-target_bed_uniformity_of_coverage_pct_0_2_mean_over_target_region`
\|\|	Coverage	Uniformity(>0.4×mean)	Percentage of sites with coverage greater than 40.0% of the mean coverage in target region.	`coverage-target_bed_uniformity_of_coverage_pct_0_4_mean_over_target_region`
\|\|	Coverage	Mean aut cov	Total number of bases that aligned to the autosomal loci in target region divided by the total number of loci in the autosomal loci in target region. If there is no autosome in the reference genome, or the target region does not intersect autosomes, this metric shows as NA.	`coverage-target_bed_average_autosomal_coverage_over_target_region`
\|\|	Coverage	Med aut cov	Median alignment coverage over the autosomal loci in target region. If there is no autosome in the reference genome or the target region does not intersect autosomes, this metric shows as NA.	`coverage-target_bed_median_autosomal_coverage_over_target_region`
\|\|	Coverage	Mean/med autosomal coverage	Mean autosomal coverage in target region divided by the median autosomal coverage in target region. If there is no autosome in the reference genome or the target region does not intersect autosomes, this metric shows as NA.	`coverage-target_bed_mean_median_autosomal_coverage_ratio_over_target_region`
\|\|	Coverage	≥1500x	Percentage of sites in target region with at least 1500x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_1500x_inf`
\|\|	Coverage	≥1000x	Percentage of sites in target region with at least 1000x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_1000x_inf`
\|\|	Coverage	≥500x	Percentage of sites in target region with at least 500x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_500x_inf`
\|\|	Coverage	≥100x	Percentage of sites in target region with at least 100x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_100x_inf`
\|\|	Coverage	≥50x	Percentage of sites in target region with at least 50x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_50x_inf`
\|\|	Coverage	≥20x	Percentage of sites in target region with at least 20x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_20x_inf`
\|\|	Coverage	≥15x	Percentage of sites in target region with at least 15x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_15x_inf`
\|\|	Coverage	≥10x	Percentage of sites in target region with at least 10x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_10x_inf`
\|\|	Coverage	≥3x	Percentage of sites in target region with at least 3x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_3x_inf`
\|\|	Coverage	≥1x	Percentage of sites in target region with at least 1x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_1x_inf`
\|\|	Coverage	≥0x	Percentage of sites in target region with any coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_0x_inf`
\|\|	Coverage	[1000x:1500x)	Percentage of sites in target region with at least 1000x but less than 1500x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_1000x_1500x`
\|\|	Coverage	[500x:1000x)	Percentage of sites in target region with at least 500x but less than 1000x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_500x_1000x`
\|\|	Coverage	[100x:500x)	Percentage of sites in target region with at least 100x but less than 500x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_100x_500x`
\|\|	Coverage	[50x:100x)	Percentage of sites in target region with at least 50x but less than 100x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_50x_100x`
\|\|	Coverage	[20x:50x)	Percentage of sites in target region with at least 20x but less than 50x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_20x_50x`
\|\|	Coverage	[15x:20x)	Percentage of sites in target region with at least 15x but less than 20x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_15x_20x`
\|\|	Coverage	[10x:15x)	Percentage of sites in target region with at least 10x but less than 15x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_10x_15x`
\|\|	Coverage	[3x:10x)	Percentage of sites in target region with at least 3x but less than 10x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_3x_10x`
\|\|	Coverage	[1x:3x)	Percentage of sites in target region with at least 1x but less than 3x coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_1x_3x`
\|\|	Coverage	0x	Percentage of sites in target region with no coverage.	`coverage-target_bed_pct_of_target_region_with_coverage_0x_1x`
\|\|	Coverage	median chr x coverage (ignore 0x regions) over target region	median chr x coverage (ignore 0x regions) over target region	`coverage-target_bed_median_chr_x_coverage_ignore_0x_regions_over_target_region`
\|\|	Coverage	median chr y coverage (ignore 0x regions) over target region	median chr y coverage (ignore 0x regions) over target region	`coverage-target_bed_median_chr_y_coverage_ignore_0x_regions_over_target_region`

WGS Coverage Metrics

Coverage metrics over genome. All samples are based on the wgs.

Press the Help button for details.

The following criteria are used when calculating coverage:

Duplicate reads and clipped bases are ignored.
DRAGEN V3.4 - 3.7: Only reads with MAPQ > min MAPQ and bases with BQ > min BQ are considered
DRAGEN V3.8 - 4.1: By default, reads with MAPQ < 1 and bases with BQ < 0 are ignored. You can use the qc-coverage-filters-n option to specify which BQ bases and MAPQ reads to filter out.

Considering only bases usable for variant calling, i.e. excluding:

Clipped bases
Bases in duplicate reads
Reads with MAPQ < min MAPQ (default 20)
Bases with BQ < min BQ (default 10)
Reads with MAPQ = 0 (multimappers)
Overlapping mates are double-counted

Showing ¹⁶/₁₆ rows and ⁵/₃₆ columns.

Sample Name	Aln reads	Reads on target	Reads on target	Aln bases	Bases on target	Bases on target	Depth	MT cov	Uniformity(>0.2×mean)	Uniformity(>0.4×mean)	Mean aut cov	Med aut cov	Mean/med autosomal coverage	≥1500x	≥1000x	≥500x	≥100x	≥50x	≥20x	≥15x	≥10x	≥3x	≥1x	≥0x	[1000x:1500x)	[500x:1000x)	[100x:500x)	[50x:100x)	[20x:50x)	[15x:20x)	[10x:15x)	[3x:10x)	[1x:3x)	0x	median chr x coverage (ignore 0x regions) over genome	median chr y coverage (ignore 0x regions) over genome
Alp13-1-20 \| Alp13-1-20	0.1M	0.1M	100.0%	19.8Mb	19.8Mb	100.0%	0.01x	0.00x	0.00%	0.00%	0.01x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	1.00	0.00
Alp13-1-100 \| Alp13-1-100	0.1M	0.1M	100.0%	18.8Mb	18.8Mb	100.0%	0.01x	0.00x	0.00%	0.00%	0.01x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	1.00	0.00
Alp22-1-20 \| Alp22-1-20	0.1M	0.1M	100.0%	18.4Mb	18.4Mb	100.0%	0.01x	0.00x	0.01%	0.01%	0.01x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	99.99%	1.00	0.00
Alp22-1-100 \| Alp22-1-100	0.1M	0.1M	100.0%	20.3Mb	20.3Mb	100.0%	0.01x	0.00x	0.01%	0.01%	0.01x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	99.99%	1.00	0.00
Alp32-1-20 \| Alp32-1-20	0.1M	0.1M	100.0%	19.4Mb	19.4Mb	100.0%	0.01x	0.00x	0.01%	0.01%	0.00x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	99.99%	2.00	0.00
Alp32-1-100 \| Alp32-1-100	0.1M	0.1M	100.0%	17.3Mb	17.3Mb	100.0%	0.01x	0.00x	0.01%	0.01%	0.00x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	99.99%	4.00	0.00
Alp42-1-20 \| Alp42-1-20	0.1M	0.1M	100.0%	19.7Mb	19.7Mb	100.0%	0.01x	0.00x	0.01%	0.01%	0.00x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	99.99%	2.00	0.00
Alp42-1-100 \| Alp42-1-100	0.1M	0.1M	100.0%	18.3Mb	18.3Mb	100.0%	0.01x	0.02x	0.01%	0.01%	0.00x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	99.99%	2.00	1.00
Alp52-1-20 \| Alp52-1-20	0.1M	0.1M	100.0%	19.9Mb	19.9Mb	100.0%	0.01x	0.00x	0.01%	0.01%	0.01x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	99.99%	1.00	0.00
Alp52-1-100 \| Alp52-1-100	0.1M	0.1M	100.0%	17.8Mb	17.8Mb	100.0%	0.01x	0.00x	0.01%	0.01%	0.00x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.01%	99.99%	1.00	0.00
Alp62-1-20 \| Alp62-1-20	0.2M	0.2M	100.0%	23.3Mb	23.3Mb	100.0%	0.01x	0.00x	0.02%	0.02%	0.01x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.02%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.02%	99.98%	1.00	1.00
Alp62-1-100 \| Alp62-1-100	0.2M	0.2M	100.0%	22.6Mb	22.6Mb	100.0%	0.01x	0.00x	0.02%	0.02%	0.01x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.02%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.02%	99.98%	1.00	0.00
AlpP2-NG011977-1-20 \| AlpP2-NG011977-1-20	0.1M	0.1M	100.0%	18.8Mb	18.8Mb	100.0%	0.01x	0.00x	0.00%	0.00%	0.00x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	6.00	0.00
AlpP2-NG011977-1-100 \| AlpP2-NG011977-1-100	0.1M	0.1M	100.0%	18.8Mb	18.8Mb	100.0%	0.01x	0.00x	0.00%	0.00%	0.00x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	2.00	0.00
AlpP3-1-20 \| AlpP3-1-20	0.1M	0.1M	100.0%	18.9Mb	18.9Mb	100.0%	0.01x	0.00x	0.00%	0.00%	0.01x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	1.00	0.00
AlpP3-1-100 \| AlpP3-1-100	0.1M	0.1M	100.0%	21.4Mb	21.4Mb	100.0%	0.01x	0.00x	0.00%	0.00%	0.01x	0.00x	infx	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%	100.00%	1.00	0.00

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: dragen-cov-metrics-own-section-wgs-table_table

Sort	Group	Column	Description	ID	Scale
\|\|	Coverage	Aln reads	Total number (millions) of aligned reads.	`coverage-wgs_aligned_reads`	read_count
\|\|	Coverage	Reads on target	Number (millions) of uniquely mapped reads to genome. DRAGEN V3.4 - V3.8: When region is the target BED, this metric is equivalent to and replaces Capture Specificity based on target region. DRAGEN V3.9 - V4.1: Only reads with MAPQ >= 1 are included. Secondary and supplementary alignments are ignored.	`coverage-wgs_aligned_reads_in_genome`	read_count
\|\|	Coverage	Reads on target	Number of uniquely mapped reads to genome relative to the number of uniquely mapped reads to the genome.	`coverage-wgs_aligned_reads_in_genome_pct`
\|\|	Coverage	Aln bases	Total number (millions) of aligned bases.	`coverage-wgs_aligned_bases`	base_count
\|\|	Coverage	Bases on target	Number (millions) of uniquely mapped bases to genome.	`coverage-wgs_aligned_bases_in_genome`	base_count
\|\|	Coverage	Bases on target	Number (millions) of uniquely mapped bases to genome relative to the number of uniquely mapped bases to the genome.	`coverage-wgs_aligned_bases_in_genome_pct`
\|\|	Coverage	Depth	Coverage depth over genome: number of uniquely mapped bases to genome divided by the number of sites in genome.	`coverage-wgs_average_alignment_coverage_over_genome`
\|\|	Coverage	MT cov	Total number of bases that aligned to the intersection of the mitochondrial chromosome with genome divided by the total number of loci in the intersection of the mitochondrial chromosome with genome. If there is no mitochondrial chromosome in the reference genome or the genome does not intersect mitochondrial chromosome, this metric shows as NA.	`coverage-wgs_average_mitochondrial_coverage_over_genome`
\|\|	Coverage	Uniformity(>0.2×mean)	Percentage of sites with coverage greater than 20% of the mean coverage in genome. Demonstrates the uniformity of coverage, the higher the better.	`coverage-wgs_uniformity_of_coverage_pct_0_2_mean_over_genome`
\|\|	Coverage	Uniformity(>0.4×mean)	Percentage of sites with coverage greater than 40.0% of the mean coverage in genome.	`coverage-wgs_uniformity_of_coverage_pct_0_4_mean_over_genome`
\|\|	Coverage	Mean aut cov	Average autosomal coverage over genome. Calculated as the number of bases that aligned to the autosomal loci in genome divided by the total number of loci in the autosomal loci in genome. If there are no autosomes in the reference genome, or the region does not intersect autosomes, this metric shows as NA.	`coverage-wgs_average_autosomal_coverage_over_genome`
\|\|	Coverage	Med aut cov	Median alignment coverage over the autosomal loci in genome. If there is no autosome in the reference genome or the genome does not intersect autosomes, this metric shows as NA.	`coverage-wgs_median_autosomal_coverage_over_genome`
\|\|	Coverage	Mean/med autosomal coverage	Mean autosomal coverage in genome divided by the median autosomal coverage in genome. If there is no autosome in the reference genome or the genome does not intersect autosomes, this metric shows as NA.	`coverage-wgs_mean_median_autosomal_coverage_ratio_over_genome`
\|\|	Coverage	≥1500x	Percentage of sites in genome with at least 1500x coverage.	`coverage-wgs_pct_of_genome_with_coverage_1500x_inf`
\|\|	Coverage	≥1000x	Percentage of sites in genome with at least 1000x coverage.	`coverage-wgs_pct_of_genome_with_coverage_1000x_inf`
\|\|	Coverage	≥500x	Percentage of sites in genome with at least 500x coverage.	`coverage-wgs_pct_of_genome_with_coverage_500x_inf`
\|\|	Coverage	≥100x	Percentage of sites in genome with at least 100x coverage.	`coverage-wgs_pct_of_genome_with_coverage_100x_inf`
\|\|	Coverage	≥50x	Percentage of sites in genome with at least 50x coverage.	`coverage-wgs_pct_of_genome_with_coverage_50x_inf`
\|\|	Coverage	≥20x	Percentage of sites in genome with at least 20x coverage.	`coverage-wgs_pct_of_genome_with_coverage_20x_inf`
\|\|	Coverage	≥15x	Percentage of sites in genome with at least 15x coverage.	`coverage-wgs_pct_of_genome_with_coverage_15x_inf`
\|\|	Coverage	≥10x	Percentage of sites in genome with at least 10x coverage.	`coverage-wgs_pct_of_genome_with_coverage_10x_inf`
\|\|	Coverage	≥3x	Percentage of sites in genome with at least 3x coverage.	`coverage-wgs_pct_of_genome_with_coverage_3x_inf`
\|\|	Coverage	≥1x	Percentage of sites in genome with at least 1x coverage.	`coverage-wgs_pct_of_genome_with_coverage_1x_inf`
\|\|	Coverage	≥0x	Percentage of sites in genome with any coverage.	`coverage-wgs_pct_of_genome_with_coverage_0x_inf`
\|\|	Coverage	[1000x:1500x)	Percentage of sites in genome with at least 1000x but less than 1500x coverage.	`coverage-wgs_pct_of_genome_with_coverage_1000x_1500x`
\|\|	Coverage	[500x:1000x)	Percentage of sites in genome with at least 500x but less than 1000x coverage.	`coverage-wgs_pct_of_genome_with_coverage_500x_1000x`
\|\|	Coverage	[100x:500x)	Percentage of sites in genome with at least 100x but less than 500x coverage.	`coverage-wgs_pct_of_genome_with_coverage_100x_500x`
\|\|	Coverage	[50x:100x)	Percentage of sites in genome with at least 50x but less than 100x coverage.	`coverage-wgs_pct_of_genome_with_coverage_50x_100x`
\|\|	Coverage	[20x:50x)	Percentage of sites in genome with at least 20x but less than 50x coverage.	`coverage-wgs_pct_of_genome_with_coverage_20x_50x`
\|\|	Coverage	[15x:20x)	Percentage of sites in genome with at least 15x but less than 20x coverage.	`coverage-wgs_pct_of_genome_with_coverage_15x_20x`
\|\|	Coverage	[10x:15x)	Percentage of sites in genome with at least 10x but less than 15x coverage.	`coverage-wgs_pct_of_genome_with_coverage_10x_15x`
\|\|	Coverage	[3x:10x)	Percentage of sites in genome with at least 3x but less than 10x coverage.	`coverage-wgs_pct_of_genome_with_coverage_3x_10x`
\|\|	Coverage	[1x:3x)	Percentage of sites in genome with at least 1x but less than 3x coverage.	`coverage-wgs_pct_of_genome_with_coverage_1x_3x`
\|\|	Coverage	0x	Percentage of sites in genome with no coverage.	`coverage-wgs_pct_of_genome_with_coverage_0x_1x`
\|\|	Coverage	median chr x coverage (ignore 0x regions) over genome	median chr x coverage (ignore 0x regions) over genome	`coverage-wgs_median_chr_x_coverage_ignore_0x_regions_over_genome`
\|\|	Coverage	median chr y coverage (ignore 0x regions) over genome	median chr y coverage (ignore 0x regions) over genome	`coverage-wgs_median_chr_y_coverage_ignore_0x_regions_over_genome`

Coverage distribution

Number of locations in the reference genome with a given depth of coverage.

Bases of a reference sequence (y-axis) are groupped by their depth of coverage (0×, 1×, …, N×) (x-axis). This plot shows the frequency of coverage depths relative to the reference sequence for each read dataset, which provides an indirect measure of the level and variation of coverage depth in the corresponding sequenced sample.

If reads are randomly distributed across the reference sequence, this plot should resemble a Poisson distribution (Lander & Waterman 1988), with a peak indicating approximate depth of coverage, and more uniform coverage depth being reflected in a narrower spread. The optimal level of coverage depth depends on the aims of the experiment, though it should at minimum be sufficiently high to adequately address the biological question; greater uniformity of coverage is generally desirable, because it increases breadth of coverage for a given depth of coverage, allowing equivalent results to be achieved at a lower sequencing depth (Sampson et al. 2011; Sims et al. 2014). However, it is difficult to achieve uniform coverage depth in practice, due to biases introduced during sample preparation (van Dijk et al. 2014), sequencing (Ross et al. 2013) and read mapping (Sims et al. 2014).

This plot may include a small peak for regions of the reference sequence with zero depth of coverage. Such regions may be absent from the given sample (due to a deletion or structural rearrangement), present in the sample but not successfully sequenced (due to bias in sequencing or preparation), or sequenced but not successfully mapped to the reference (due to the choice of mapping algorithm, the presence of repeat sequences, or mismatches caused by variants or sequencing errors). Related factors cause most datasets to contain some unmapped reads (Sims et al. 2014).

Created with MultiQC

Cumulative coverage hist

Number of locations in the reference genome with at least given depth of coverage.

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

Coverage per contig

Average coverage per contig or chromosome. Calculated as the number of bases (excluding duplicate marked reads, reads with MAPQ=0, and clipped bases), divided by the length of the contig or (if a target bed is used) the total length of the target region spanning that contig.

Created with MultiQC

Coverage per contig (non-main)

Non-main contigs: unlocalized (random), unplaced (chrU), alts (*_alt), mitochondria (chrM), EBV, HLA. Zoom in to see more contigs as all labels don't fit the screen.

Created with MultiQC

Fragment length hist

Distribution of estimated fragment lengths of mapped reads per read group. Only points supported by at least 5 reads are shown to prevent long flat tail. The plot is also smoothed down to showing 300 points on the X axis to reduce noise.

Created with MultiQC

Trimmer Metrics

Metrics on trimmed reads.

Showing ¹⁶/₁₆ rows and ³⁰/₃₀ columns.

Sample Name	Total input reads	Total input bases	Total input bases R1	Total input bases R2	Average input read length	Remaining poly-G K-mers R2 3prime	Poly-G soft trimmed reads unfiltered R1 3prime	Poly-G soft trimmed reads unfiltered R2 3prime	Poly-G soft trimmed bases unfiltered R1 3prime	Poly-G soft trimmed bases unfiltered R2 3prime
Alp13-1-20 \| Alp13-1-20	136886	20199121	10101347	10097774	147	0.0	0.0	0.1	0.0	0.0
Alp13-1-100 \| Alp13-1-100	127526	19049236	9528179	9521057	149	0.0	0.0	0.1	0.0	0.0
Alp22-1-20 \| Alp22-1-20	124804	18673778	9339487	9334291	149	0.0	0.0	0.1	0.0	0.0
Alp22-1-100 \| Alp22-1-100	137870	20648414	10327940	10320474	149	0.0	0.0	0.1	0.0	0.0
Alp32-1-20 \| Alp32-1-20	132436	19850478	9919811	9930667	149	0.0	0.0	0.2	0.0	0.1
Alp32-1-100 \| Alp32-1-100	118542	17734911	8861551	8873360	149	0.0	0.0	0.2	0.0	0.1
Alp42-1-20 \| Alp42-1-20	135068	20092736	10057545	10035191	148	0.1	0.0	0.5	0.0	0.1
Alp42-1-100 \| Alp42-1-100	125326	18681019	9352566	9328453	149	0.1	0.0	0.5	0.0	0.2
Alp52-1-20 \| Alp52-1-20	134678	20197797	10103002	10094795	149	0.0	0.3	0.2	0.0	0.1
Alp52-1-100 \| Alp52-1-100	120162	18031718	9019542	9012176	150	0.0	0.3	0.2	0.0	0.1
Alp62-1-20 \| Alp62-1-20	159672	23874811	11948726	11926085	149	0.0	0.0	0.2	0.0	0.1
Alp62-1-100 \| Alp62-1-100	154422	23087419	11555418	11532001	149	0.0	0.0	0.3	0.0	0.1
AlpP2-NG011977-1-20 \| AlpP2-NG011977-1-20	133116	19332887	9668555	9664332	145	0.0	11.0	0.1	0.6	0.0
AlpP2-NG011977-1-100 \| AlpP2-NG011977-1-100	129634	19164264	9584550	9579714	147	0.0	12.7	0.1	0.7	0.0
AlpP3-1-20 \| AlpP3-1-20	135936	19405531	9697906	9707625	142	0.0	0.0	0.1	0.0	0.0
AlpP3-1-100 \| AlpP3-1-100	148190	21813954	10902454	10911500	147	0.0	0.0	0.1	0.0	0.0

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: dragen-trimmer-metrics-table_table

Sort	Column	Description	ID
\|\|	Total input reads	Total input reads	`trimmer_metrics-Total_input_reads`
\|\|	Total input bases	Total input bases	`trimmer_metrics-Total_input_bases`
\|\|	Total input bases R1	Total input bases R1	`trimmer_metrics-Total_input_bases_R1`
\|\|	Total input bases R2	Total input bases R2	`trimmer_metrics-Total_input_bases_R2`
\|\|	Average input read length	Average input read length	`trimmer_metrics-Average_input_read_length`
\|\|	Total trimmed reads	Total trimmed reads	`trimmer_metrics-Total_trimmed_reads`
\|\|	Total trimmed bases	Total trimmed bases	`trimmer_metrics-Total_trimmed_bases`
\|\|	Average bases trimmed per read	Average bases trimmed per read	`trimmer_metrics-Average_bases_trimmed_per_read`
\|\|	Average bases trimmed per trimmed read	Average bases trimmed per trimmed read	`trimmer_metrics-Average_bases_trimmed_per_trimmed_read`
\|\|	Remaining poly-G K-mers R1 3prime	Remaining poly-G K-mers R1 3prime	`trimmer_metrics-Remaining_poly_G_K_mers_R1_3prime`
\|\|	Remaining poly-G K-mers R2 3prime	Remaining poly-G K-mers R2 3prime	`trimmer_metrics-Remaining_poly_G_K_mers_R2_3prime`
\|\|	Poly-G soft trimmed reads unfiltered R1 5prime	Poly-G soft trimmed reads unfiltered R1 5prime	`trimmer_metrics-Poly_G_soft_trimmed_reads_unfiltered_R1_5prime`
\|\|	Poly-G soft trimmed reads unfiltered R1 3prime	Poly-G soft trimmed reads unfiltered R1 3prime	`trimmer_metrics-Poly_G_soft_trimmed_reads_unfiltered_R1_3prime`
\|\|	Poly-G soft trimmed reads unfiltered R2 5prime	Poly-G soft trimmed reads unfiltered R2 5prime	`trimmer_metrics-Poly_G_soft_trimmed_reads_unfiltered_R2_5prime`
\|\|	Poly-G soft trimmed reads unfiltered R2 3prime	Poly-G soft trimmed reads unfiltered R2 3prime	`trimmer_metrics-Poly_G_soft_trimmed_reads_unfiltered_R2_3prime`
\|\|	Poly-G soft trimmed reads filtered R1 5prime	Poly-G soft trimmed reads filtered R1 5prime	`trimmer_metrics-Poly_G_soft_trimmed_reads_filtered_R1_5prime`
\|\|	Poly-G soft trimmed reads filtered R1 3prime	Poly-G soft trimmed reads filtered R1 3prime	`trimmer_metrics-Poly_G_soft_trimmed_reads_filtered_R1_3prime`
\|\|	Poly-G soft trimmed reads filtered R2 5prime	Poly-G soft trimmed reads filtered R2 5prime	`trimmer_metrics-Poly_G_soft_trimmed_reads_filtered_R2_5prime`
\|\|	Poly-G soft trimmed reads filtered R2 3prime	Poly-G soft trimmed reads filtered R2 3prime	`trimmer_metrics-Poly_G_soft_trimmed_reads_filtered_R2_3prime`
\|\|	Poly-G soft trimmed bases unfiltered R1 5prime	Poly-G soft trimmed bases unfiltered R1 5prime	`trimmer_metrics-Poly_G_soft_trimmed_bases_unfiltered_R1_5prime`
\|\|	Poly-G soft trimmed bases unfiltered R1 3prime	Poly-G soft trimmed bases unfiltered R1 3prime	`trimmer_metrics-Poly_G_soft_trimmed_bases_unfiltered_R1_3prime`
\|\|	Poly-G soft trimmed bases unfiltered R2 5prime	Poly-G soft trimmed bases unfiltered R2 5prime	`trimmer_metrics-Poly_G_soft_trimmed_bases_unfiltered_R2_5prime`
\|\|	Poly-G soft trimmed bases unfiltered R2 3prime	Poly-G soft trimmed bases unfiltered R2 3prime	`trimmer_metrics-Poly_G_soft_trimmed_bases_unfiltered_R2_3prime`
\|\|	Poly-G soft trimmed bases filtered R1 5prime	Poly-G soft trimmed bases filtered R1 5prime	`trimmer_metrics-Poly_G_soft_trimmed_bases_filtered_R1_5prime`
\|\|	Poly-G soft trimmed bases filtered R1 3prime	Poly-G soft trimmed bases filtered R1 3prime	`trimmer_metrics-Poly_G_soft_trimmed_bases_filtered_R1_3prime`
\|\|	Poly-G soft trimmed bases filtered R2 5prime	Poly-G soft trimmed bases filtered R2 5prime	`trimmer_metrics-Poly_G_soft_trimmed_bases_filtered_R2_5prime`
\|\|	Poly-G soft trimmed bases filtered R2 3prime	Poly-G soft trimmed bases filtered R2 3prime	`trimmer_metrics-Poly_G_soft_trimmed_bases_filtered_R2_3prime`
\|\|	Total filtered reads	Total filtered reads	`trimmer_metrics-Total_filtered_reads`
\|\|	Reads filtered for minimum read length R1	Reads filtered for minimum read length R1	`trimmer_metrics-Reads_filtered_for_minimum_read_length_R1`
\|\|	Reads filtered for minimum read length R2	Reads filtered for minimum read length R2	`trimmer_metrics-Reads_filtered_for_minimum_read_length_R2`

Time Metrics

Time metrics for DRAGEN run. Total run time is less than the sum of individual steps because of parallelization.

Created with MultiQC

DRAGEN-FastQC

Illumina Bio-IT Platform that uses FPGA for secondary analysis of sequencing data.https://www.illumina.com/products/by-type/informatics-products/dragen-bio-it-platform.html

Per-Position Mean Quality Scores

The mean quality value across each base position in the read.

To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

Taken from the FastQC help:

The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

Created with MultiQC

Per-Sequence Quality Scores

The number of reads with average quality scores. Shows if a subset of reads has poor quality.

From the FastQC help: The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

Created with MultiQC

Sequence Length Distribution

The distribution of fragment sizes (read lengths) found. See the FastQC help

Created with MultiQC

Per-Sequence GC Content

The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

From the FastQC help: This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content. In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution. An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

Created with MultiQC

GC Content Mean Quality Scores

The mean quality value across each base position in the read.

To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

Taken from the FastQC help:

Created with MultiQC

Per-Position N Content

The percentage of base calls at each position for which an N was called.

From the FastQC help: If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called. It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

Created with MultiQC

Per-Position Sequence Content

The proportion of each base position for which each of the four normal DNA bases has been called.

To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor. To see the data as a line plot, as in the original FastQC graph, click on a sample track. From the FastQC help: Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called. In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other. It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

Click a sample row to see a line plot for that dataset.

Rollover for sample name

Position: -

%T: -

%C: -

%A: -

%G: -

Adapter Content

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

Note that only samples with ≥ 0.1% adapter contamination are shown.

There may be several lines per sample, as one is shown for each adapter detected in the file.

From the FastQC Help:

The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

Created with MultiQC

PCRpanel amplicon sequencing QC (DRAGEN, hg38)

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PCRpanel amplicon sequencing QC (DRAGEN, hg38)

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General Statistics

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DRAGEN

Mapping metrics

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Mapped / paired / duplicated

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Sequence Length Distribution

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