In this study, we analysed > 500 isolated of S. cerevisiae to calculate the linkage disequilibrium among the chromosomes. From the LD decay plots, it can be shown that the evolutionary history for each chromosome varies. LD was analysed and compared with all the 16 chromosomes of the budding yeast S. cerevisiae, and we found out the different effects LD have on various chromosomes. The data was analysed by Illumina sequencing and compared to the already accessible data in the gene banks to identify SNPs and short indels by the Department of Molecular Biotechnology and Microbiology. GATK was used to perform the local alignment around the indels and variant calling. GATK was used to produce gVCF file for almost > 500 isolates of S. cerevisiae where the PSB was used. After mapping with bwa, BAM files were created, which were further converted to compressed VCF by GATK.