In .sam file, how can I know if an alignment is ambiguous. (A read is mapped to multiple places)?
Forgive me if this can be found in SAM's Spec.
In flag 0x0100 shows the alignment is not primary, which should have a different meaning. Even it is primary, does it mean it is the only mapping or there are other place that the read mapped.
I haven't found other field that provide the information. It should be there, right?
Forgive me if this can be found in SAM's Spec.
In flag 0x0100 shows the alignment is not primary, which should have a different meaning. Even it is primary, does it mean it is the only mapping or there are other place that the read mapped.
I haven't found other field that provide the information. It should be there, right?
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