Table 2.

The false positive and false negative rates of the CQ method

Data set	Total autosome and X sequences	Autosome or X sequences with CQ < 0.3	False positive rate	Total Y sequences	Y sequences with CQ <0.3	False negative rate
H. sapiens	621,581	135	2.44%	7,934	5,408	31.8%
D. melanogaster	66,881	2	1.85%	139	106	23.7%

The false positive rate is highly dependent on the CQ cut-off below which a sequence is classified as Y-linked. In this study, we used a CQ cut-off of 0.3 as it minimized false positives while keeping false negatives relatively low. There is flexibility in selecting the CQ cut-off according to the focus of the study and the scale of downstream verification that the investigators plan to perform.