|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|
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