User Messages - FASTQ and alignment QC

User messages are intended to easily and conveniently alert the user of any quality standard that was not met for the analysis

VarSome Clinical has introduced a system to easily deliver accessible messages to the users about the quality of the input data in their samples. These messages are presented both on the "Dashboard" / "Samples" and "Variant table", per sample and provide useful information about the status of each sample during the step of quality control.

Quality control is performed at the FASTQ (FASTQC tool) and the BAM level, to ensure that the raw data is good enough to reliably analyze the results. For each analysis, warning or error icons may appear on the "Samples" / "Dashboard" menu to inform the users that the quality control of the FASTQ file produced warnings and/or errors.


To reduce the number of error/warning messages displayed on the “Samples”/ “Dashboard” menu and improve their practicality, FASTQC errors have been divided into three groups according to their frequency: Frequent, Standard and Rare. The Frequent messages include Per base sequence content as well as Per sequence GC content. Frequent errors will not display any warning or error message, therefore their messages will not appear as warnings or errors on the "Samples" / "Dashboard" menu. 

On the other hand, Standard errors include:

  • Per tile sequence quality
  • Overrepresent sequences
  • Adapter Content
  • Sequence Duplication Levels

and will display a single warning when there is more than two present in the report. 

Note: Sequence Duplication Levels will be ignored when the analysis used an amplicon kit. 

Finally, Rare errors include:

  • Per base sequence quality
  • Per base N content
  • Per sequence quality scores
  • Sequence Length Distribution

and will display an error message when there is one or more of them present in the report.


To know more about what parameters of FASTQC have risen the flag, you can click on the icons, and a pop-up window will appear showing you a detailed description.

The same information is also available in the variants table for an individual analysis:

In the same way, there are some quality checks run at the alignment level that will produce warnings and/or error messages in case there are issues with the coverage of the sample.