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Old 01-28-2011, 02:26 AM   #1
ganga.jeena
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Location: INDIA

Join Date: Jun 2010
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Default Regarding Solexa data

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
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Old 02-03-2011, 08:29 AM   #2
seb567
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Location: Québec, Canada

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Default

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 !
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