Hi! What encoding is used for fastq files from ncbi sequence read archive? ANSII, UTF8?
Are you referring to the format of the SRA files themselves or the actual fastq files that are converted to SRA (and back)? File formats for SRA are described here.
Fastq files themselves are always ascii encoded. However, you get sra files from SRA (you can convert these to fastq, of course).
SRA provides SRA files. You can find some additional info on the SRA format here: http://www.ncbi.nlm.nih.gov/books/NBK158900/