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MrOlm / inStrain

Bioinformatics program inStrain
MIT License
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what`s the meaning of the no data between the gene #172

Closed lori1996 closed 2 weeks ago

lori1996 commented 8 months ago
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Hello, I have some output files (SNV.tsv) that don't understand. Could you please help me with it~ I see the document to explain the gene of the SNV.tsv-"If a gene file was included, this column will be present listing if the SNV is in the coding sequence of a gene". So, if this is no data, it means this SNV not in genes? but according to my outfiles, the position 4839 of this no data SNV is inclued in the MP9-1-complete-150_ctg297528_56x_c_3 gene. Why the position is in this gene, this SNP is detected in non-gene?

MrOlm commented 8 months ago

Hi @lori1996 - two possible explanations. 1) are you running an old version of inStrain? That could explain it. 2) Is it a "cryptic" SNV? If so, that could explain it.

Best, Matt

lori1996 commented 8 months ago

@MrOlm thank your reply. I checked the version of my software, its v1.8.0. and Im sorry that I don`t understand the mean of cryptic SNV, how can I know the SNV is cryptic or how can I detect cryptic SNV?

MrOlm commented 8 months ago

Apologies for not being more clear- there should be a column in the SNVs.txt file specifying if it’s a cryptic SNV or not