The precision of CNV breakpoint mapping determines how reliably mutation mechanisms might be inferred. We determined the precision of our breakpoint estimates by identifying 350 CNVs in two samples (194 breakpoints in NA15510 and 156 in NA12878) for which breakpoint sequences have been published18,19,25. Comparing our breakpoint estimates to these sequences revealed excellent precision (median estimation error ~60 bp), representing an improvement of more than an order of magnitude over previous population-based CNV surveys8, with similarly accurate estimation for both samples (NA15510: 1 bp–17.1 kb, median 54 bp; NA12878: 0 bp–5.5 kb, median 62 bp). These findings were supported by high-concordance of breakpoint estimation between replicate experiments (Supplementary Methods).
