Namechecker and Positionconverter interpret n. as c.
Created by: mutalyzerbot
Original ticket: https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/144 Original date: 2013/08/22 Original reporter: I DOT F DOT A DOT C DOT Fokkema AND LUMC DOT nl
Both the Namechecker and the Position converter are interpreting n. notation as c., and therefore make calculation mistakes.
Example:[[BR]] Position converting NM_022988.2:n.554_565del on mm10 returns:
NC_000067.65:g.58450507_58450518del
Nif3l1: NM_022988.2:c.554_565del
Expected (NM_022988 has an upstream sequence of 30):
NC_000067.65:g.58450477_58450488del
Nif3l1: NM_022988.2:c.524_535del
The Name checker does the same. Example:[[BR]] https://mutalyzer.nl/check?name=NM_022988.2%3An.554_565del [[BR]] Returns:
Raw variant 1: deletion of 584 to 595
Description relative to transcription start:
NM_022988.2:n.584_595del
Which then links to a page that results in:[[BR]] NM_022988.2:n.614_625del [[BR]] Which then links to a page that results in:[[BR]] NM_022988.2:n.644_655del [[BR]] etc, etc.
Expected:
Raw variant 1: deletion of 554 to 565
Description relative to transcription start:
NM_022988.2:n.554_565del
Which then links to a page that results in exactly the same output.