Next generation sequencing (NGS) has emerged as an important tool towards marker discovery. Single nucleotide polymorphisms (SNPs) are the markers of choice and occur with a very high frequency in lower vertebrates including fishes, differing from other forms of variation in their extent, origin and functional impact. In this study, we have used 10 wild rohupopulations collected from different geographical regions of India. Low depth next generation sequencing has been done using Illumina Nextseq 500 platform taking 3 individuals from each population generating 60 GB (40X) raw sequence data. A good quality assembly of rohu genome with 95% genome coverage was used as reference genome for the current study. Mapping of reads of each wild population with the reference was done using a fully automated pipeline namely Variant Discovery and Annotation Tool-Graphical User Interface (VDAP-GUI). The SNPs were determined by using three programs SAMtools, VarScan and FreeBayes. A total of 4.95 million SNPs were identified from all the 10 populations. Number of SNPs ranged from 3,80,991 to 6,79,963 in each population, and number of common SNPs between any two populations ranged from 1,00,743 to 2,00,764. The results of this study is very useful for marker assisted selection, SNP array development and genome-wide association studies.