In this study, we are planning to apply deep coverage genome sequencing to some of the S. cerevisiae isolates to explore their diversity in mitochondrial copy numbers. We are planning to use different types of S. cerevisiae isolates which came from different origins like fermentation, nature and human origin. Genomes used in this study were sequenced in earlier studies or come from the collection of the Department of Biotechnology and Microbiology. The Department’s Yeast Lab conducted the mapping of Illumina reads, converting them to BAM files and coverage mapping using BedTools. It is one of the aims to give a glance at how it is possible to write a script full of commands which we can use along with different software and different tools to convert FASTQ files into SAM/BAM files and use them in mapping and coverage analysis.