| Popis: |
Additional file 1: Figure S1. Heatmap showing % average nucleotide identities (ANI) similarities among the different strains and populations in the 30 mock communities. Figure S2. Validating MetaPop���s macrodiversity and codon bias analyses. (A) Tornado plot showing the relative abundances of Staphylococcus aureus, Staphylococcus epidermidis, and Bacillus subtilis across the 30 mock communities in the actual synthesized community and as determined by MetaPop. Bar charts contained within the gray bar to the left of the tornado plot reveal the number strains per each bacterial species, with three being the highest number of strains per species. (B) Boxplots showing median and quartiles of different ��-diversity indices (richness, Shannon���s H, and Peilou���s J) compared between the actual and MetaPop derived abundances. The Wilcoxon test p-values above are the result from comparing actual and MetaPop derived ��-diversity indices. (C) Heatmaps of ��-diversity Bray-Curtis dissimilarity distances calculated using the actual and MetaPop derived abundances. Figure S3. Genome map of genes with outlier codon usage in ST5 Staphylococcus aureus ECT-R2. Figure S4. Validating MetaPops���s microdiversity analyses using the Global Oceans Virome 2 dataset. (A-E, right) Line plots sorted by the original average nucleotide diversity (��) values from [20] and (A-E, left) scatter plots comparing the average �� for the Tara Oceans stations in the GOV2 dataset derived from the (A) original GOV2 values versus MetaPops���s PHRED���30 local SNP calls, (B) original GOV2 values versus MetaPops���s PHRED���30 global SNP calls, (C) original GOV2 values versus MetaPops���s PHRED���20 global SNP calls, (D) MetaPops���s PHRED���20 global SNP calls versus MetaPops���s PHRED���30 global SNP calls, and (E) MetaPops���s PHRED���30 global SNP calls versus MetaPops���s PHRED���30 local SNP calls. The dashed line in the scatter plot represents the linear regression. (F, left to right) Bar plots showing the biological microdiveristy trends across the ecological zones defined in [20] derived from the original GOV2 values, MetaPops���s PHRED���20 global SNP calls, MetaPops���s PHRED���30 global SNP calls, and PHRED���30 local SNP calls. Figure S5. Scatterplots with Loess smoothing displaying runtime per sample for the rate-limiting part of MetaPop (i.e. pre-processing and the SNP calling section of microdiversity) as a factor of file size in megabytes on (left and right) the biological datasets and (center) the synthetic dataset. |
