Case flags in the CIP-API and Interpretation Portal¶
A case may have one or more of the following flags applied:
| 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. |