> 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/tso500/dragen-tso-500-guides/dragen-tso-500-v2.6/overview-1/quality-control/run-qc.md).

# Run QC

## Run QC

The Run Metrics section of the metrics output report provides sequencing run quality metrics along with suggested values to determine if they are within an acceptable range. The overall percentage of reads passing filter is compared to a minimum threshold. For Read 1 and Read 2, the average percentage of bases ≥ Q30, which gives a prediction of the probability of an incorrect base call (Q‑score), are also compared to a minimum threshold. The following tables show run metric and quality threshold information for different systems.

The values in the Run Metrics section are listed as NA in the following situations:

* If the analysis was started from FASTQ files.
* If the analysis was started from BCL files and the InterOp files are missing or corrupt.

### NextSeq 500/550 or NextSeq 550Dx (RUO)

| Metric             | Description                                         | Recommended Guideline Quality Threshold | Variant Class |
| ------------------ | --------------------------------------------------- | --------------------------------------- | ------------- |
| PCT\_PF\_READS (%) | Total percentage of reads passing filter.           | ≥80.0                                   | All           |
| PCT\_Q30\_R1 (%)   | Percentage of Read 1 reads with quality score ≥ 30. | ≥80.0                                   | All           |
| PCT\_Q30\_R2 (%)   | Percentage of Read 2 reads with quality score ≥ 30. | ≥80.0                                   | All           |

### NovaSeq 6000 or NovaSeq 6000Dx (RUO)

| Metric             | Description                                         | Recommended Guideline Quality Threshold | Variant Class |
| ------------------ | --------------------------------------------------- | --------------------------------------- | ------------- |
| PCT\_PF\_READS (%) | Total percentage of reads passing filter.           | ≥55.0                                   | All           |
| PCT\_Q30\_R1 (%)   | Percentage of Read 1 reads with quality score ≥ 30. | ≥80.0                                   | All           |
| PCT\_Q30\_R2 (%)   | Percentage of Read 2 reads with quality score ≥ 30. | ≥80.0                                   | All           |

### NextSeq 1000/2000

| Metric           | Description                                         | Recommended Guideline Quality Threshold | Variant Class |
| ---------------- | --------------------------------------------------- | --------------------------------------- | ------------- |
| PCT\_Q30\_R1 (%) | Percentage of Read 1 reads with quality score ≥ 30. | ≥85.0                                   | All           |
| PCT\_Q30\_R2 (%) | Percentage of Read 2 reads with quality score ≥ 30. | ≥85.0                                   | All           |

### NovaSeq X

| Metric           | Description                                         | Recommended Guideline Quality Threshold | Variant Class |
| ---------------- | --------------------------------------------------- | --------------------------------------- | ------------- |
| PCT\_Q30\_R1 (%) | Percentage of Read 1 reads with quality score ≥ 30. | ≥85.0                                   | All           |
| PCT\_Q30\_R2 (%) | Percentage of Read 2 reads with quality score ≥ 30. | ≥85.0                                   | All           |


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