The Flux Simulator provides some statistical indicators to measure the u=
niformity of the read distribution along a transcript produced by *in si=
lico* sequencing.

The fraction of a transcript that is covered by reads reflects its expre= ssion and the degree of of coverage fluctuation provoked by biases.

where is the length of the transcript,

and the sign function

indicating whether a position is covered by at least one sequenced read.=

Pearson=E2=80=99s chi-square can be used to test the goodness of fit of = a given sample to a theoretical distribution. Given a transcript of length = and coverage at position , the test statistic is defined as fo= llows:

where is the average coverage along the molecule.

A CV is defined as the ratio of the standard deviation and the standard = deviation of a probability distribution:

, with standard deviation and mean

of transformed coverage values

Latter Anscombe transformation of coverage values has been proposed [Hansen et al. 2010] under= the assumption that the distribution of reads along a transcript follows a= Poisson distribution, which is to be transformed to a Gaussian distributio= n.