Referral Flags

If during processing, a case triggers a pre-defined QC check, they are automatically flagged. The table below lists the flags, a brief description and where they can be seen in the Interpretation Portal.

If you have any concerns or questions relating to case flags, please email the ge-servicedesk@genomicsengland.co.uk and quote the case identifier (e.g. patient ID or referral ID) and the flag.

Please see Genomics England Rare Disease Genome Analysis Guide v2.0 for further information regarding case flags.

Note

Flag	Description
LOW COVERAGE	<95% of the autosomal genome covered at ≥15x calculated from reads with mapping quality >10 and >85x10^9 bases with Q≥30, after removing duplicate reads and overlapping bases after adaptor and quality trimming.
SALIVA SAMPLE	Genome sequencing performed using DNA extracted from saliva. There is a risk of poorer quality sequencing data for saliva samples.
UNUSUAL SEX KARYOTYPE	At least one member of the family has a sex karyotype that is not XX or XY
INCORRECT OR DISCORDANT SEX KARYOTYPE	Reported karyotypic and phenotypic sex are discrepant but the karyotypic sex is supported by the sex inferred from the genomic data in at least one family member
INFERRED GENETIC AND REPORTED SEX DISCORDANT	Reported sex is discrepant from the inferred genetic sex and the Disorders of Sex development panel has been applied
UNKNOWN PHENOTYPIC SEX	Phenotypic sex is unknown for at least on member of a family
POOR QUALITY CNV CALLS	Majority of CNV calls in the proband are expected to be of poor quality
SUSPECTED POOR QUALITY CNV CALLS	An increased number of poor quality CNV calls is suspected
'ddddddddd [mat|pat]UPDnn [i|h|m][c|p]'	Uniparental disomy detected that segregates with disease.

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Last update: 2022-06-14