Looking at the overall copy number changes (page 2), we see that we have a duplication (3 copies), 2 deletions (1 copy) and a copy neutral section.
Looking at the copy number per allele (page 1), we see that:
- The duplication is compose of the A allele in 2 copies and the B allele in 1 copy.
- The deletions show the presence of the A allele in 1 copy and the absence of the B allele.
- The copy neutral section is only composed of the A allele in 2 copies and the absence of the B allele
From this results it is likely that, in fact:
- the full chromsome is triploid (2 A + 1 B)
- there is a massive deletion of the B copy (130-166 Mb)
- there are 2 smaller deletions of one of the A copies (130-135 Mb and 140 Mb)