Regarding Solexa data

[ganga.jeena]

What exactly does the following mean:

63_k/nohup.out

Output 285695310 out of 495475004 (57.7)% reads in gaps
352330547 out of 495475004 (71.1)% reads mapped to contigs

Regards,
Ganga Jeena

[seb567]

Gaps refer to the stretches of unidentified nucleotides between contigs in your scaffolds.

Perhaps the obvious is implied -- you have reads that align in gaps.

I presume that this means that these reads don't align on contigs and therefore it is presumed that they belong in the gaps.

Could be contamination too !