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.

Hall et al.

Hall et al. BMC Genomics 2013 14:273   doi:10.1186/1471-2164-14-273

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