Whole Genome Sequencing QC Report

1. Project Overview

Total Samples

10

WGS libraries

Total Input Reads

6,647.6M

across all samples

Avg Mapped Reads

98.06%

DRAGEN mapping

Avg Duplicate Rate

15.10%

duplicate marked

Avg Mean Depth

26.08x

genome coverage

Avg Q30 Bases

96.47%

base quality

Avg GC Content

40.49%

FastQC GC

Median Insert Size

377

bp

Study Design: Whole genome sequencing libraries were processed with the DRAGEN DNA pipeline, including adapter trimming, read mapping, duplicate marking, coverage estimation, and variant calling. QC metrics were aggregated with MultiQC for cross-sample review. This report showcases standard, extended, and customized capabilities; availability depends on sample type, study design, and project scope.

Pipeline Overview

Step	Tool	Output Directory
Raw read QC	FastQC + MultiQC	`01.QualityCheck/`
Alignment	DRAGEN mapper	`02.BamFiles/`
Duplicate marking	DRAGEN duplicate marking	`02.BamFiles/`
Variant calling	DRAGEN DNA pipeline	`03.SNV_VCF/`

2. Sample Information

#	Sample ID	Customer ID
1	Sample-1	NA12878_DNA
2	Sample-2	HG0002
3	Sample-3	HG0003
4	Sample-4	HG001
5	Sample-5	GM12878
6	Sample-6	HCC1954
7	Sample-7	NA24385
8	Sample-8	NA19240
9	Sample-9	K562
10	Sample-10	HeLa

3. Methods

DRAGEN DNA pipelines are selected based on study design: Germline WGS (blood/saliva/normal samples), Tumor-only somatic, and Tumor–Normal paired somatic workflows. All pipelines share core steps (read mapping, duplicate marking, QC aggregation), while somatic analyses add additional filters and modeling specific to tumor context. Reference genome: GRCh38; annotations via VEP v113 where included.

QC metrics are aggregated with MultiQC, and downstream deliverables include BAMs, annotated SNV VCFs, and optional extended outputs (SV, CNV, joint genotyping) when requested.

4. QC Summary (MultiQC)

Per-sample metrics summarized from multiqc_report.html.

Sample	Input Reads (M)	Mapped %	Duplicate %	Properly Paired %	Median Insert	Q30 %	Mean Depth (x)	≥20x %	≥10x %	GC %	Ploidy
Sample-1	667.1	98.12	15.09	97.61	373	96.42	26.18	85.16	93.36	40.45	XX
Sample-2	664.6	98.09	15.38	97.42	376	96.41	25.97	82.08	93.25	40.52	XY
Sample-3	657.9	98.14	15.42	97.55	378	96.45	25.80	84.42	93.37	40.51	XX
Sample-4	648.2	98.04	14.87	97.47	362	96.58	25.55	83.65	93.40	40.50	XX
Sample-5	593.9	97.92	14.97	97.36	383	96.44	23.20	73.76	92.59	40.48	XY
Sample-6	699.7	98.12	16.53	97.61	397	96.23	27.11	87.19	93.61	40.48	XX
Sample-7	710.1	98.00	16.73	97.51	405	96.19	27.34	87.39	93.44	40.47	XX
Sample-8	740.0	98.05	15.80	97.45	386	96.28	28.69	86.37	93.68	40.47	XY
Sample-9	650.7	97.99	14.80	97.43	367	96.62	25.66	84.01	93.43	40.47	XX
Sample-10	615.5	98.11	11.44	97.44	288	97.11	25.26	80.33	93.15	40.54	XY

5. Coverage Metrics

Coverage metrics summarize sequencing depth and uniformity across the genome, highlighting breadth at common depth thresholds (e.g., ≥20x, ≥10x).

Avg Depth

26.08x

mean alignment coverage

Uniformity (0.2×)

94.15%

sites above 0.2× mean

Uniformity (0.4×)

93.06%

sites above 0.4× mean

≥20x Genome

83.44%

average across samples

≥10x Genome

93.33%

average across samples

6. Variant Summary

Variant summary highlights total variant counts and composition (SNPs vs indels), along with Ti/Tv and Het/Hom ratios as high-level quality indicators.

Avg Total Variants

5.31M

per sample

Avg SNPs

81.29%

of total variants

Avg Indels

17.97%

of total variants

Avg Ti/Tv

1.90

transition/transversion

Avg Het/Hom

1.69

heterozygous/homozygous

Avg Filtered

0.64%

filtered variants

Variant metrics are summarized from DRAGEN variant calling statistics in MultiQC. Detailed VCFs are provided in 03.VCF/.

7. Standard Deliverables

File Path	Description
`01.QualityCheck/*.csv`	DRAGEN QC metrics tables (Germline v4.4.4)
`01.QualityCheck/multiqc_report.html`	Aggregated QC report
`02.BamFiles/*.bam`	Aligned reads with duplicates marked
`03.SNV_VCF/*.anno.vcf.gz`	Annotated SNV VCFs (DRAGEN + VEP v113)
`03.SNV_VCF/somatic.vcf.gz`	Somatic SNV VCFs (tumor/normal paired or tumor-only)

8. Extended Analyses

Copy Number Variation

CNV detection is available through DRAGEN CNV and CNVpytor workflows. For tumor-normal paired samples, purity/ploidy estimation and CNV segmentation are performed with DRAGEN.

$CNVpytor comparison plot$

Figure 4 includes two panels from the updated high-quality CNVpytor output.

Structural Variation

Structural variants are detected using DRAGEN SVcaller or Delly2, leveraging paired-end and split-read signals for accurate breakpoint discovery.

Extended Deliverables

File Path	Description
`04.SV/`	Structural Variant VCFs (DRAGEN Germline v4.4.4 or Delly2 v1.3.1)
`05.CNV/`	CNV results (DRAGEN CNV or CNVpytor 1.3.1; includes `.vcf`, `.pytor`)
`06.JointVCF/`	Joint genotyping VCFs (DRAGEN Joint Genotyping v4.4.4)

9. Customized Analyses

Customized analyses are tailored to project-specific goals. Availability depends on sample type and experimental design and may require additional data or validation.

Output	Description
`08.Denovo/`	Per-family joint VCFs with potential de novo mutations
`09.plasmid_insertion/`	Potential plasmid insertion sites
`10.kraken_taxanomy_analysis/`	Taxonomy profiling of unmapped reads (Kraken2 PlusPF-16)
`11.custom_Plots/`	Project-specific plots (Circos, Waterfall/Oncoplot)

Below are example customized plots. Figure 5 and Figure 6 are different Circos views (SV/CNV and SV/CNV/Translocations). Figure 7 is a Waterfall/Oncoplot commonly used in tumor analyses.

Figure 5: Circos plot of CNV and Translocations

Figure 6: Circos plot of SV, CNV, and Translocations

Figure 7: Waterfall/Oncoplot of tumor variants

10. References

Resource	Link
DRAGEN DNA Pipeline Guide	https://help.Dragen.illumina.com
VEP Predicted Data	https://useast.ensembl.org/info/genome/variation/prediction/predicted_data.html
DRAGEN CNV Documentation	https://help.Dragen.illumina.com/product-guides/Dragen-v4.3/Dragen-dna-pipeline/cnv-calling/cnv-output
CNVpytor Documentation	https://github.com/abyzovlab/CNVpytor/wiki/4.-Genotyping-genomic-regions
DRAGEN SV Documentation	https://help.Dragen.illumina.com/product-guides/Dragen-v4.3/Dragen-dna-pipeline/sv-calling#structural-variant-vcf-output

Whole Genome Sequencing Quality Control Report