Why is the name of the generated consensus sequence same as the reference accession number?
A title of a consensus sequence depends on a program that you use to calculate the consensus. An accession number is a reasonable variant for a title.
How to deal with the situation if the name of consensus sequence generated from a sample is changed to the same as reference sequence after consensus generation?
FASTA files are just text files, you can change their headers any way you like. Don't you know how to edit text files?
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