what`s the meaning of the no data between the gene

[lori1996]

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]

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]

@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]

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