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10x Genomics
GemCode Genome & Exome

Run Alerts: Interpretation

The Loupe ALERTS view highlights issues in the sequencing data that users should be aware of. Alerts are generally the result of factors inherent in library construction and sequencing instead of software. Alerts cover common short-read sequencing metrics and GemCode-specific statistics. The navigation bar will display a colored Alerts link when alerts are present for the sample.

Alerts come in two severity levels:

If alerts are triggered a ALERTS view tab is added to the header.

Here is an example Loupe ALERTS view.