Below is an explanation of each type of file we provide.
.ab1 Files: The .ab1 file is the chromatogram (trace) file from your sample. By viewing this file type you’ll be able to see the actual peaks associated with each base call. Programs to use: There are a number of different programs that can be used to view these files. We have links to a couple of these, here.
.raw.seq.txt: This is an untrimmed fasta file. This file is not edited and may contain some low quality base calls. It’s important to verify these calls by viewing the .raw.qual.txt quality score file or the peaks in the chromatogram.
.raw.qual.txt: This file lists the phred quality score of each base in the .raw.seq.txt file.
Probability of Error = 10^(-Quality Score/10)
So a quality score of 20+ means there’s less than a 1% chance of error.
seq.txt: This is the trimmed version of the fasta file. In this file, high quality bases with phred scores above 20 are capitalized, low quality bases are in lower case. Low quality bases are trimmed off the start and ends of the sequences. Wells that have no high quality bases are omitted from this file.
seq.qual.txt: This file lists the phred quality score of each base in the trimmed seq.txt file.
Seq.info.txt: This file lists information on read lengths and quality scores for each well.