HI,

I am writing my thesis partly with MG-Rast (and getting a taste of metagenomic analysis as stressing as it has been) and i realized an inconsistency in the "hits" on the Json and the "hits" on the graphed data, after re-reading the documentation i got to the conclusion it must be divided (or a reducing of some kind) by the abundance. My issue is that i cannot find the abundance in any file, and as such i cannot correlate one with the other, and in the documentation, they talk about an avundace column in the tables... but i dont have any table in the server, and those made with the API-JSON do not show abundance.

Here is obvious the discrepancies, and even the relevance is different. I tried checking withe CSV file that one can download per statistic, but the information is not particularly understandable

Another issue is that assuming that the species list present in the JSON are not modified later, then there is something weird with the Shannon index operation: i calculated the Shannon independently and i got the same value MG-Rast gives me if i use ln instead of log10 (and in the documentation it is explained that the alpha diversity is given by 10^Shannon).

I am probably just be mixing it all up, in which case i am sorry but i can´t find my answer anywhere else.

I kindly beg for you help and thank you for your time,

Rebeca H