Base abbreviations other than ACTGU in sequence file
I usually convert SRA files to FASTQ before doing any further processing, but the tooling for converting SRA files is cumbersome.
To simplify things, I recommend you download the FASTQ file directly. The ENA currently has a nicer interface for doing these things. Here is a link to download the FASTQ files for the SRA sequencing run associated with the SRA experiment you are describing: https://www.ebi.ac.uk/ena/browser/view/SRR11588968
A description of the FASTQ format can be found here: https://en.wikipedia.org/wiki/FASTQ_format