Copy Number Variant Read-Depth Detector

Sequencing Sample

Sequencing noise σ (log2) 0.15

CNV events on chromosome 3

Detection Algorithm

Smoothing window (bins) 5

Call threshold |log2 ratio| 0.35

Live Detection Stats

Sensitivity

Precision

Called segments (true events)

0 (0)

How it works

Whole-genome sequencing reads are counted in fixed-size genomic windows ("bins"). For a diploid genome the expected read count per bin is proportional to copy number 2. A copy-number variant (CNV) shifts the local copy number, which shifts the observed depth:

log2 ratio(bin) = log2( observed_depth / expected_depth )
CN = 2 (normal)   → ratio = 1.0   → log2 = 0
CN = 1 (deletion) → ratio = 0.5   → log2 = -1.0
CN = 3 (duplication) → ratio = 1.5 → log2 = +0.58

Raw per-bin log2 ratios are noisy, so real callers (CBS, HMM-based tools like CNVkit) smooth the signal before thresholding. This simulator uses a simple moving-average smoother of width W bins, then calls a bin a CNV if the smoothed value exceeds the threshold T:

smoothed[i] = mean( log2[i-W/2 .. i+W/2] )
called[i]   = |smoothed[i]| > T

Sequencing noise σ — the standard deviation of per-bin depth noise; lower coverage / worse library prep raises σ and buries small events.
CNV events — how many deletion/duplication segments are randomly placed along the simulated chromosome.
Smoothing window — larger W rejects more noise but blurs the boundaries of short events and can miss them entirely.
Call threshold — raising T reduces false positives from noise spikes but also reduces sensitivity to true, subtle CNVs.
Sensitivity / Precision — computed against the (otherwise hidden) ground-truth CNV placement, exactly as a benchmark against a truth set would score a real caller.

Clinical relevance: CNV calls like this feed directly into personalized medicine — a deleted tumor-suppressor gene, an amplified oncogene (e.g. HER2), or a duplicated pharmacogene changes both diagnosis and drug dosing.

Normal (CN=2) Called deletion Called duplication Uncalled / noise

⚠ Couldn't load the 3D engineThree.js failed to load from the CDN. Check your connection and reload.