Methods, systems and processes of identifying genetic variations

A method of genome analysis comprising:

• a) generating single-end sequence reads obtained from an entire genome of a subject, wherein (i) the reads represent less than 5% of the entire genome, (ii) the average distance between the reads is at least 4000 bp, and (iii) the reads comprise sequence information for greater than 400,000 polymorphisms, each read comprising the sequence information for at least one of the polymorphisms;
• b) determining a presence or absence of heterozygosity for each of the polymorphisms according to the sequence information;
• and
• c) determining the presence or absence of a copy number variation (CNV) for a portion of the genome according to the presence or absence of heterozygosity determined in (b).