About the explanation of annotation output

[ClarenceHsiang]

Dear dellytools team,

Thank you for providing the convenient tool "dellytools." Regarding the interpretation of the annotation results, I have some questions and would like to confirm them with you further.

1. Example 1, Pmu.1_1G000010(739;+)
   Does the first number refer to the position 739 downstream of the gene body, or the position 739 downstream of the translation start site for Pmu.1_1G000010?
2. Example 2, Pmu.1_1G000110(-947;-)
   On the contrary, does Pmu.1_1G000110(-947;-) refer to the position 947 upstream of the gene body, or the translation start site?
3. Example 3,Pmu.1_1G000120(0;-)
   When it's 0, does it refer to being within the gene body, or does it signify something else?
4. What does "query.ct" mean?

Sincerely yours,

Clarence