Microbial dispersal in the subseafloor

Additional files, including the contigs, anvi’o protein calls, Prodigal protein calls, and anvi’o database profiles for the MAGs. Along with Dataset files. <br> Supplemental Data Legend <strong>Supplemental Data S1.</strong> MAG quality values with details on relationship to original Tully \textit{et al.} (2018) MAGs. <br> <strong>Supplemental Data S2.</strong> MAG RPKM values in all time points of interest using variable identity cutoffs in the BamM step. Each MAG is also assessed for the number of samples it is "present" in using different RPKM cutoff values. <br> <strong>Supplemental Data S3.</strong> MAG values for total SNVs, length, SNV per kbp, nucleotide diversity, and T:P ratio. <br> <strong>Supplemental Data S4.</strong> inStrain results for each genome by time point of interest. <br> <strong>Supplemental Data S5.</strong> The set of inStrain linkage.csv and SNVs.tsv used to calculated linkage disequilibrium. <br> <strong>Supplemental Data S6.</strong> For each MAG, the genes that were determined to have variable coverage across time points. Gene IDs and coverage values determined from anvi'o output. Top two BLAST matches in the NR database are provided for each gene and KEGG assignment (when available). <br> <strong>Supplemental Data S7.</strong> For each MAG, genes determined to be have statistically significant differences in nucleotide diversity, as a proxy for putative genes that have undergone a selective sweep. Significance determined by Welch's t-test. Mean dN/dS was determined from Gretel results. <br> <strong>Supplemental Data S8.</strong> Output for the Gretel analysis. There is a directory for each gene from each MAG with the raw Gretel results. <br> <strong>Supplemental Data S9.</strong> Output for the PAML analysis There is a directory for each gene from each MAG based on the Gretel results. <strong>Supplemental Data S10.</strong> Reports the population mean FST values for genes that met cutoff criteria. Calculated in a pairwise manner between time points of interest. Reports the genes and region number when 5+ genes were detected with mean FST &gt;1 standard deviation above the genome mean. Reports the genes and region number when 5+ genes were detected with mean FST &gt;2 standard deviation above the genome mean. When relevant includes corresponding data from Supplemental Data 7. Performed in a pairwise manner between time points of interest. Reports num. of SNV per gene, FST, p, and coverage. <br> <strong>Supplemental Data S11.</strong> Provides information on the KEGG categories of genes determined to have putative selective sweeps.