Running variants detection in CLC for virus quaisspecies results in 2 tables, being:

1. One with rows numbers matching the number of variants informed by CLC, including alleles found in reference.

2. An annotated table, in which only alleles different from the reference are included and with a rows number circa half of the above.

I assume the "real" variants numbers are only those found in 2. as in 1. the master sequence alleles are also included.

Am I correct?

Thanks