Why Consensus sequence output is as same as refrence genome?

05 March 2023 1 7K Report

After obtaining bam file, I used bcftools to perform vcf, then using bcftools consensus command line included its parameter such as refrence genome, vcf.gz file, the output file with fasta format obtained but its header and appearance is alike the refrence genome fasta format. Is it correct or something is wrong?

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