Commands > Reads
The fastq_eestats command reports statistics on
quality scores and expected errors.
See fastq_eestats2 for a related
command which generates a more readable summary.
The report is written to a tabbed text file specifed by the
-output option. The distribution Phred (quality) scores and expected errors is
reported in terms of the mean and
Fields in the tabbed text file are:
Pos: zero-based position in the read.
Reads: number of reads that include this position.
PctRecs: fraction of reads that include this position, as a percentage.
Min_Q: Minimum Q score.
Low_Q: Lower quartile Q score.
Med_Q: Median Q score.
Mean_Q: Mean Q score.
Hi_Q: Upper quartile Q score.
Max_Q: Maximum Q score.
Min_EE: Minimum EEs.
Low_EE: Lower quartile EEs.
Med_EE: Median EEs.
Mean_EE: Mean EEs.
Hi_EE: Upper quartile EEs.
Max_EE: Maximum EEs.
Here, EEs means the total expected errors for positions zero
through the current position. The tabbed text file can be loaded into a
spreadsheet or other program for generating plots of read quality as in the
example below where light green=below lower quartile, dark green=lower quartile,
black line=median, red=upper quartile, yellow=above upper quartile.
usearch -fastq_eestats reads.fastq -output eestats.txt