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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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What's the meaning of KWWM and SCTWW in the assembled sequences? #188

Closed CS-CH closed 1 year ago

CS-CH commented 2 years ago

Hi, I find there are some special signs such as KWWM and SCTWW in the assembled sequences, and the mapping coverage at these sites seems extremely low. I am wondering if the linkage relationship of these regions could be accepted. Thank you!

ndierckx commented 2 years ago

HI, These are IUPAC codes, so positions that couldn't be called accurately This could be variation but in your case it are probably homopolymers (illumina has low quality in these regions) http://www.bioinformatics.org/sms2/iupac.html

What you mean by "linkage relationship of these regions could be accepted."?