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Jenna M. Lang deleted file Results - Sequencing.md
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##Sequence Processing and Summary Statistics
The number of high-quality sequences per meal ranged from 168,669-318,956. After OTU assignment, mitochondrial and chloroplast sequences were filtered out, and sequences that were observed only once (globally) were removed. After filtration, the range of sequences per sample decreased to 974-279,136. All subsequent diversity analyses were performed on samples that were rarefied to 974 sequences per sample.
##Taxonomic Composition and Diversity of the Different Dietary Patterns
In terms of taxonomic richness (both measured by number of OTUs and phylogenetic diversity,) there was no significant difference between diet types (Fig) (non-parametric Kruskal-Wallis test with compare\_alpha\_diversity.py, P>0.6). We also tested for the significant variation in frequency of individual OTUs between diet types using the Kruskal-Wallis test as implemented in the group_significance.py script. Before conducting these tests, we removed OTUs that were not present in at least 3 of the 15 samples. None of the OTUs were significantly different between the three diet types.
