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-   -   Indeterminate nucleotides ? (http://seqanswers.com/forums/showthread.php?t=93567)

BlendSkill 03-25-2020 12:19 PM

Indeterminate nucleotides ?
 
Hello !
I am a French student and I am very interested in DNA sequencing.
I downloaded the sequenced human genome (in Fasta format) from the "U.S. National Library of Medicine" to study it.
Approximately 7% of the nucleotides are replaced by the letter N, which means that it's Adenine, Cytosine, Guanine OR Thymine, so it's indeterminate.

Could someone explain to me how it's possible to have indeterminate nucleotides?
Nobody answered me on the French forums or on the less specific American forums.

Thank you in advance :)

GenoMax 03-26-2020 04:24 AM

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.

BlendSkill 03-26-2020 10:36 AM

Thank you very much !


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