Chao1 estimates are identical to observed richess, when using phyloseq, is this accurate?

Question

[will.wcb]

Hey all,

When I use the estimate_richness in function in phyloseq in R, the given Chao1 values are identical to our observed richness. There is not a single point of difference.

I was wondering what this might mean? Is our sampling depth truly perfect? Or is there some problem that this is indicative of.

I haven't normalized or trimmed the data in any way prior to performing this analysis.

Thank you, please let me know if you need more info.

[Fabio Marroni]

Check in the raw classification data if you have species represented by only one or two reads. Those are the species that cause differences between the two measures. The result is indeed strange because the probability that you have a species represented only by one read is high (e. g. due to sequencing errors).