The alpha rarefication analysis for control.

The alpha rarefication analysis was used to determine if the richness of samples has been fully observed or sequenced. The alpha diversity rarefication plot was included (S2 File -> alpha_rarefaction -> rarefaction.qzv) to illustrate different rarefication measurements such as Shannon and number of OTUs. It showed that richness of all treatments was achieved with sequence depth of about 10000 reads. All treatments received sequencing depth that was much more 70,000. This suggested that the analysis discovered all microbes in these samples. Statistical tests of Shannon indices were included (S2 File -> Shannon_group_significance.qzv). PC analysis of reference sequence categorized by samples was included in the output qzv file (S2 File -> beta_rarefaction -> weighted_unifrac.qzv) using weighted UniFrac distance.
(ZIP)