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Old 03-26-2020, 04:24 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
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Rather then indeterminate, N signifies that a reliable base call is not possible at that location.

N's are also included to indicate locations where current sequencing technologies are unable to sequence DNA (think of telomeres, centromeres etc which may have homopolymeric/repeat stretches). So we know there is DNA there but don't know the actual sequence. So keep the length of the chromosome roughly the same as what we expect N's are padded to the sequence.
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