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katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens
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result interpretation #111

Closed capricy closed 5 years ago

capricy commented 5 years ago

Dear SRST2 Team,

I have questions about the outputs of gene typing:

  1. genescombined.SPI__results.txt contains "" and "?". What are those symbols mean?

  2. *fullgenescombined.SPI__results.txt contains annotation column and some of records is not empty. What is the information in this column?

Examples are in the attached image file:

screen shot 2018-09-01 at 9 13 50 pm

Thanks.

Kind regards,

C.

katholt commented 5 years ago

Hi Capricy,

See readme - https://github.com/katholt/srst2#gene-typing ? indicates uncertainty due to low depth in some parts of the gene

The annotation is pulled from the gene database that you are using. Some DBs have annotations and some don't.