Note that the first parent is contested, as the clade is reported to be BA.4, while the most likely lineage is BA.5.2.1*. This conflict is also seen in the first parent's confidence, which is low at 0.28.
To draw attention to this, I could create a new field called parent_conflict. If a parent_lineage is not a descendant of the corresponding parent_lineage, this field could be set to true.
At first, this will just be a field for exploratory purposes. But if it appears to help with identifying false positives, this could be a default filter to excluded samples with parent conflict.
Conflict has been observed between the populations reported between
parent_cladeandparent_lineage. Example:Omicron/BA.4/22A,Omicron/BA.2.12/22CBA.5.2.1*,BA.2.12.1*0.28,0.688Note that the first parent is contested, as the clade is reported to be
BA.4, while the most likely lineage isBA.5.2.1*. This conflict is also seen in the first parent's confidence, which is low at0.28.To draw attention to this, I could create a new field called
parent_conflict. If aparent_lineageis not a descendant of the correspondingparent_lineage, this field could be set totrue.At first, this will just be a field for exploratory purposes. But if it appears to help with identifying false positives, this could be a default filter to excluded samples with parent conflict.