Illumina reads with dots

[naumenko.sa]

Some reads from Illumina (qseq file) have dots at the beginning and in the middle of the read.
......CTTTTTAAGCCACAGCATGCTCAGGAAGTTACGATATTGCAAAGGATTTACTGTGACGTGGGTGAAATGTTACTCTCCTCCGATATTGCTGTAACCGATCA..TCAAACCCT.TGGCGA.TT.AGAGTCAAAGCCCATTACCAGCTGCGCCTAC
What does it mean?

[kmcarr]

It means that the base caller was unable to determine the base at that position. When the reads are converted to FASTQ format the dots will be replaced with N's.

[naumenko.sa]

Thank you, kmcarr.