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Table 2 The false positive and false negative rates of the CQ method

From: Six novel Y chromosome genes in Anophelesmosquitoes discovered by independently sequencing males and females

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%

  1. 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.
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BMC Genomics

ISSN: 1471-2164

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