based on poisson distribution, probability of each nucleotide will be sequenced is P(Y=y)= (Cy)(e-c)/y!
y=number of times base is sequenced
C= coverage =NL/G = (#reads)(length of read)/genome size
if y=0 it mean that from the equation, I will get probability of no nucleotide sequenced because of 0 time each base sequenced
make probability into percentage is just multiply by 100, Now I got %nucleotide base that is NOT sequenced
I understood that this percentage multiply by genome size equal to total number of nucleotide that is NOT sequenced (total gap length) but I cannot imagine how
"the percentage multiply by number of reads equal to number of gap" WHY
there are more explanation about my question here
http://www.illumina.com/documents/products/technotes/technote_coverage_calculation.pdf
go to page 2, last paragraph
thank you in advance
Chooseel
In that document, the number calculated with a gap of 0.2% is referred to the genome size used in the example: one of aprox. 3 Gb. But this is big size. Another example is if we want to sequence a genome of 4 Mb (4.000.000) (near average for a bacterial genome), thus if I obtained, for instance 800.000 reads each one of 100bp, then you have in total information 80.000.000 bp (80 Mb), this is 20X coverage of the targeted genome. The distribution of gaps may not change significantly depending of the size of the reads (if the total information is the same) but it really affects the assembly. If you want to do a nearly complete assembly of a genome, using different programs available for it, you may need a minimum of 25X coverage if the average on reads is 250bp, but you may need more than 120X if the reads are of 100bp.
@ Howard Junca Thank you for your recommendation but I still don't understand why the percentage multiply by number of reads equal to number of gap. I cannot answer my homework question LOL.
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