> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section/quality-metrics-per-variant-type/sv-quality-metrics.md).

# SV quality metrics

The following metrics are calculated for structural variants.

Structural variant callers use breakpoint clusters, depth shifts, and split-read evidence to compute quality. Large structural variants can fail quality thresholds even when the underlying biology is real.

### **VCF Filter** (DRAGEN 4.3+)

* The FILTER column value in VCF indicating whether a variant passed the caller's quality thresholds or failed some checks.

### **Quality**

* Represents the variant quality score as provided in the VCF.

### **Size**

* Indicates the length of the structural variant.

### **Bin Count**

* Represents the number of bins supporting the structural variant call.

### **CIPOS**

* Start breakpoint confidence interval
* Extracted from `VCF INFO: CIPOS` and displayed as two integers `[lower, upper]`. The interval width (upper - lower) determines the confidence level of the start breakpoint:
  * High (0–20)
  * Moderate (21–100)
  * Low (>100)
* Available from v100.40.0+ versions.

### **CIEND**

* End breakpoint confidence interval
* Extracted from `VCF INFO: CIEND` and displayed as two integers `[lower, upper]`. The interval width (upper - lower) determines the confidence level of the end breakpoint:
  * High (0–20)
  * Moderate (21–100)
  * Low (>100)
* Available from v100.40.0+ versions.

### **Paired Read Support (PR)**

* Extracted from `VCF FORMAT: PR`.
  * `PR[0]` indicates number of paired reads supporting the reference allele (`REF`)
  * `PR[1]` indicates number of paired reads supporting the alternate (`ALT`) structural variant allele.
* Available from v100.40.0+ versions.

### **Split Read Support (SR)**

* Extracted from `VCF FORMAT: SR`.
  * `SR[0]` indicates number of split reads supporting the reference allele (`REF`)
  * `SR[1]` indicates number of split reads supporting the alternate (`ALT`) allele.
* Available from v100.40.0+ versions.


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