Background: Structural Variations, SVs, in a genome can be linked to a disease or characteristic phenotype. The variations come in many types and it is a challenge, not only determining the variations accurately, but also conducting the downstream statistical and analytical procedure. Method: Structural variations, SVs, with size 1 base-pair to 1000s of base-pairs with their precise breakpoints and single-nucleotide polymorphisms, SNPs, were determined for members of a family. The genome was assembled using optimal metrics of ABySS and SOAPdenovo assembly tools using paired-end DNA sequence. Results: An interesting discovery was the mitochondrial DNA could have paternal leakage of inheritance or that the mutations could be high from maternal inheritance. It is also discovered that the mitochondrial DNA is less prone to SVs re-arrangements than SNPs, which propose better standards for determining ancestry and divergence between races and species over a long-time frame. Sex determination of an individual is found to be strongly confirmed using calls of nucleotide bases of SVs to the Y chromosome, more strongly determined than SNPs. We note that in general there is a larger variance -and thus the standard deviation, in the sum of SVs nucleotide compared to sum of SNPs of an individual when compared to reference sequence, and thus SVs serve as a stronger means to characterize an individual for a given trait or phenotype or to determine sex. The SVs and SNPs in HLA loci would also serve as a medical transformation method for determining the success of an organ transplant for a patient, and predisposition to diseases apriori.