Table 2.

Rate of de novo CNVs in XHMM/CANOES overlapping calls and XHMM and CANOES exclusive calls

	CANOES exclusive	XHMM/CANOES overlap	XHMM exclusive
Total number of calls in probands	187	355	166
de novo (percentage of total)	3 (1.6%)	10 (2.8%)	39 (23.5%)

This table compares the number of total and high confidence de novo CNV calls in the XHMM (quality ≥ 57)/CANOES (quality ≥ 0) overlapping set, the XHMM (quality ≥ 57) exclusive set and the CANOES (quality ≥ 80) exclusive set. The CANOES quality threshold of 80 was selected because at this quality threshold CANOES makes nearly the same number of calls in probands as does XHMM at 57. A call was considered to be de novo in a child at a certain threshold if its ‘SQ’ quality exceeded the threshold and the ‘NQ’ quality in each parent also exceeded the threshold.