I was searching for human mitochondrial reference genome but i didn't find it. Please tell me where i can find it? Is it available somewhere or not?
It's included as "chrM" or "MT" in the "normal" reference genomes such as hg38 that you can get from Ensembl or GENCODE.
For example https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/ -- use Homo_sapiens.GRCh38.dna.chromosome.MT.fa.gz
https://docs.varsome.com/en/mito-genome-versions
The standard mitochondrial genome is the revised Cambridge Reference Sequence (rCRS), GenBank number: NC_012920.1. This is the mitochondrial sequence included in the hg38 human genome. However, the older hg19 genome contains NC_001807.4 instead.
Also, check out MITOMAP. There, you will find all the information about the chrM, including references, haplotypes, methods, and tools.
From where i can get annotation file for mitochondrial reference genome NC_012920.1
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