Average Q is a bad idea!
FASTQ format options
Cock et ail
(2010) paper describing FASTQ
FASTQ files are text files containing sequence data with a
quality (Phred) score for each base,
represented as an ASCII character. The quality score
is an integer (Q) which is typically in the range 2 - 40, but higher and lower
values are sometimes used. In particular, versions 1.8 and later of the Illumina
platform generate reads with Q scores up to 41.
Unfortunately, the FASTQ format is not standardized. There are several variants
in common use, and it is not possible to distinguish them automatically with
high reliability. The fastq_chars command can be
used to guess the format of an unknown file. See
FASTQ format options.
FASTQ read with 50nt in Illumina format (ASCII_BASE=33).
There are always four lines per read. The first line starts with '@',
followed by the label.
The third line starts with '+'. In some variants, the '+' line contains a
second copy of the label.
The fourth line contains the Q scores represented as ASCII characters.