Calculating sequence coverage

[tahamasoodi]

How can we calculate the coverage of Illumina paired end whole genome sequencing data using Waterman equation? Example data is given:

Total reads = 450,000,000
Read length = 101
Genome size = 3000000000

[lorendarith]

http://www.illumina.com/Documents/pr...alculation.pdf

The Lander/Waterman equation is a method for computing coverage.
The general equation is:

C = LN / G

• C stands for coverage
• G is the haploid genome length
• L is the read length
• N is the number of reads

So, if we take one lane of single read human sequence with v3 chemistry, we get

C = (100 bp)*(189×10^6)/(3×10^9 bp) = 6.3

This tells us that each base in the genome will be sequenced between six and seven times on average.

---------------------

Though take care whether the "total reads" number is really the number of all reads (read 1 + read 2) or actually the "total pair" number. In the first case, you can just do the equation, however if it's the latter then you need to

C = 2*LN/G

[tahamasoodi]

How can we know whether it is total number or paired number?