  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.
