Alpha Diversity measures are the same


I have been running the qiime diversity alpha-rarefaction plugin to get metrics for chao1, goods_coverage, shannon, and observed_otus. For some of the projects that I have been running recently, some of the metrics have the same numbers. For one project, chao1 and goods_coverage had the same numbers and for another project chao1 and shannon had the same numbers. Is this a possible bug?

Thank you

Hey there @bensarawichitr!

How about you provide us with some more context? Are you saying you saw the same values across different samples? Across different projects? Please take a few minutes to write something detailed up. Thanks! :t_rex:


Here is an example of what I'm talking about:

The values are the same for each metric for the each sample. Having chao1 and observed_otus have the same value does not make any sense. In the other project the values of chao1 and shannon are the same for each sample.

How are you generating the feature table used to compute these metrics? DADA2? Deblur? OTU Clustering?

If you used DADA2 to produce your feature table, you should be aware that DADA2 does not produce singleton ASVs. Let’s take a look at the formula for chao1:


where F1 and F2 are the count of singletons and doubletons, respectively.

This reduces to chao1=S_{obs} when F1 is zero, which is the case when using DADA2. I think that explains your results. TLDR, you probably shouldn’t compute chao1 on DADA2-produced ASV table. If you didn’t use DADA2, please let us know.


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