# Does my sequencing run look good?
Overall sequencing run performance is evaluated by determining whether the sequencing run meets the Illumina specifications for quality scores and data output. Actual run performance will vary based on sample type, quality, and clusters passing filter. Specifications are based on the Illumina [PhiX](https://github.com/illumina-swi/illumina-knowledge/blob/master/articles/Knowledge/What-is-the-PhiX-Control-v3-Library-and-what-is-its-function-in-Illumina-Next-Generation-Sequencing-support-bulletin/README.md) control library at [Cluster density guidelines](/instrumentation/general/instrumentation-general-reference_material-list/000001511.md).
**Where can I find instrument specifications?**
Follow the links below to the instrument specification pages:
[iSeq 100](https://www.illumina.com/systems/sequencing-platforms/iseq/specifications.html) | [MiniSeq](https://www.illumina.com/systems/miniseq/specifications.html) | [MiSeq](http://www.illumina.com/systems/miseq/performance_specifications.html) | [MiSeq i100 Series](https://www.illumina.com/systems/sequencing-platforms/miseq-i100/specifications.html) | [NextSeq 500/550](http://www.illumina.com/systems/nextseq-sequencer/performance-specifications.html) | [NextSeq 1000/2000](https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000/specifications.html) | [NovaSeq 6000](https://www.illumina.com/systems/sequencing-platforms/novaseq/specifications.html) | [NovaSeq X Series](https://www.illumina.com/systems/sequencing-platforms/novaseq-x-plus/specifications.html)
The [Sequencing Analysis Viewer](http://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.html) (SAV) is a free software used to assess the performance of sequencing runs, and can be downloaded from the Illumina website:
* SAV v3.0 Supports the NovaSeq X Series, MiSeq i100 Series and NextSeq 1000/2000 XLEAP runs
* SAV v2.5.12 Supports NextSeq 1000/2000 on Control Software v1.5 and later with Standard reagents (for XLEAP reagents use SAV v3.0)
* SAV v2.4.7 Supports all instruments except Linux based instruments (MiSeq i100 Series, NovaSeq X Series and NextSeq1000/2000)
Once SAV is installed, open it and select the tab containing the desired query information.
**Note:** SAV 3.0 tabs have different names from previous versions, but with the same information: the Analysis tab (v2.5.12 or earlier) is the same as the Charts tab (v3.0), while the Summary tab (v2.5.12 or earlier) is the same as the Metrics tab (v3.0).
**How do I determine if my run meets spec?**
Below is an example of a PhiX validation run (2 x 151 bp) on the MiSeq, using v2 reagents. The specifications for this kit (MiSeq v2 300 cycles) are as follows:
* Total data output of 4.5-5.1 gigabases (Gb)
* At least 80% of bases called with a quality score of 30 or higher (at least 80% ≥ Q30)
To determine the quality score, review the Analysis tab Q score Distribution chart and the Summary tab as shown below.
-Analysis Tab (Charts tab in SAV 3.0):
-Summary Tab (Metrics tab in SAV 3.0):
The run had a total **Q30** of 94.09% with a total **yield** of 6.10 Gb and meets quality specification for this kit (Q30 ≥ 80%; yield >4.4 Gb).
**What additional information can I obtain from SAV?**
The following images are from [BaseSpace public data set](https://basespace.illumina.com/datacentral): “MiSeq: Nextera DNA Flex (replicates of *E. coli, B. cereus*, and *R. sphaeroides*)”. Note: Nextera DNA Flex has been renamed to [Illumina DNA Prep](https://support.illumina.com/sequencing/sequencing_kits/illumina-dna-prep/documentation.html).
**Figure 1.** Analysis Tab: Overview of the run metrics.
1. Flow Cell Chart shows color-coded metrics per tile for the entire flow cell.
2. Data by Cycle displays various metrics for each cycle of the run. Select the displayed metric, lane, surface, and channel using the drop-down lists.
3. Q Score Distribution shows a quick overview of the quality of the run. The Q30 for the whole run is found in the upper right of this box.
4. Data by Lane shows plots of metrics per lane.
5. Q score Heatmap displays a heat map for Q score by cycle.
**Figure 2.** Imaging Tab: Displays thumbnails from the run if available.
1. Toggle which base or color channel image to view here.
2. If thumbnails are saved for the run, they are displayed here.
**Figure 3.** Summary Tab: Provides basic data quality metrics summarized per lane and per read.
1. Run summary per read, including quality, is reported here.
2. More details per read including the exact density, clusters Passing Filter (PF), and % aligned.
**Figure 4.** Indexing Tab: Total and Per Sample % Reads Identified if a sample sheet was used and demultiplexing was performed.
1. Metrics for the entire run. Note: % Reads Identified will not include any PhiX because PhiX is not indexed.
2. Metrics per sample, using indexing information from the sample sheet.
3. Graph plotting the percent of reads identified for each sample present in the sample sheet.
**Additional Resources:**
* * [Sequencing Analysis Viewer Software Guide](https://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav/documentation.html)
* [Sequencing Analysis Viewer (SAV) Training](https://support.illumina.com/content/dam/illumina-support/courses/sav-overview/story_html5.html)
* [Plotting %Occupied by %PF to optimize loading for the NovaSeq 6000 and X, MiSeq i100, and iSeq 100](/instrumentation/general/instrumentation-general-reference_material-list/000002308.md)
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| *For any feedback or questions regarding this article (Illumina Knowledge Article #1922), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002308%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |
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