Hi everyone,
I have some Illumina GA fastq files with base quality values that don't span the full range that I expect.
The quality values for each of five lanes have the following ranges:
lane 1: 2 to 27
lane 2: -1 to 26
lane 3: 1 to 24
lane 4: 1 to 27
lane 5: 0 to 30
with the majority of bases in all lanes having quality values 22 or 23.
I got the values above by subtracting the offset 64=='@' from the ascii values of the chars presented in the fastq files.
These ranges don't seem to be consistent with anything I've seen elsewhere. For example, with Solexa quality values I think the range should go from -5 to 40, and for Phred quality values 0 to 40.
[ Side note: I am not certain whether my files contain Solexa or Phred-based quality values. I see that the quality value output in GERALD fastq files has changed since Illumina pipeline 1.3 (http://seqanswers.com/forums/showthread.php?t=1110). Since lane 2 contains some -1's, I assume my quality values are Solexa ]
Anyone have any ideas about what could be happening here? Why don't I see any bases with qualities higher than 30?
Thanks!
Dan
________
I have some Illumina GA fastq files with base quality values that don't span the full range that I expect.
The quality values for each of five lanes have the following ranges:
lane 1: 2 to 27
lane 2: -1 to 26
lane 3: 1 to 24
lane 4: 1 to 27
lane 5: 0 to 30
with the majority of bases in all lanes having quality values 22 or 23.
I got the values above by subtracting the offset 64=='@' from the ascii values of the chars presented in the fastq files.
These ranges don't seem to be consistent with anything I've seen elsewhere. For example, with Solexa quality values I think the range should go from -5 to 40, and for Phred quality values 0 to 40.
[ Side note: I am not certain whether my files contain Solexa or Phred-based quality values. I see that the quality value output in GERALD fastq files has changed since Illumina pipeline 1.3 (http://seqanswers.com/forums/showthread.php?t=1110). Since lane 2 contains some -1's, I assume my quality values are Solexa ]
Anyone have any ideas about what could be happening here? Why don't I see any bases with qualities higher than 30?
Thanks!
Dan
________
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