Unfortunately you are correct, we are not really sequencing the genome. We are simply reading short segments of DNA, and comparing that to a reference sequence

Unfortunately you are correct, we are not really sequencing the genome. We are simply reading short segments of DNA, and comparing that to a reference sequence to find point mutations (eg. changes from G to C). We cannot easily determine whether there are large-scale duplications with the present technology. Ironically, the older, more expensive tech was better at this. There is so much variation missed by "genome sequencing" that it is no surprise to me that we can only explain a tiny percentage of heritable human variation with genetics. See: http://www.nature.com/nature/journal/v461/n7265/full/nature08494.html http://www.nature.com/nature/journal/v461/n7265/full/nature0... for more.