Okay, so I found the source of confusion, the reciprocal of r is called \alpha.
So DESeq2 reports this \alpha. I guess zero dispersion suggests that variance and mean are same that is \mu = \sigma^2. So it is no longer a negative binomial distribution. A possible hack I can think of is putting a very small value to navigate divide by zero overflow. Please suggest if there is a better way.

The variance can then be written m + m2/r. Some authors prefer to set α = 1/r, and express the variance as m + α m2. In this context, and depending on the author, either the parameter r or its reciprocal α is referred to as the “dispersion parameter”, “shape parameter” or “clustering coefficient”,[5] or the “heterogeneity”[4] or “aggregation” parameter.[6] The term “aggregation” is particularly used in ecology when describing counts of individual organisms. Decrease of the aggregation parameter r towards zero corresponds to increasing aggregation of the organisms; increase of r towards infinity corresponds to absence of aggregation, as can be described by Poisson regression.

Tagging: Michael Love

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