[BiO BB] quasispecies or ambiguities

[Mhmoud Elhefnawi]

Dear members,
I have sequences after PCR and direct sequencing of some hepatitis c virus from patients.
The sequencer output has some positions that are A/g, or C/t etc...I want to know if these represent quasispecies or ambiguities? and if they represent quasispecies,  what is the best way  to deal with that? to write all different  combinations of these in the sequence as different quasispecies or what?
Thank you all in advance for your kind assistance,
Mahmoud
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