Supplementary data for publication Global distribution of mcr gene variants in 214K metagenomic samples

# Supplementary data for the manuscript "Global distribution of mcr gene variants in 214,095 metagenomic samples" SD1_mapped_runids.csv : tab-separated file with columns of run_accessions downloaded from ENA and whether the metagenome were positive for at least one of the mcr genes. SD2_mcr_df.csv : compositional table of mcr-positive metagenomes with associated metadata (collection_year, country, and host) for each run_accession, as well as mapping results. SD3_mcr_contigs.fa : FASTA file with contigs carrying mcr genes. The header contains the run_accession ID. SD4_aldex2_results.csv: CSV file containing ALDEx2 results. The columns are as follows:<br> * group: metadata category (year, country or host). If the column contains more than one label, e.g., "Denmark - 2020 - Pigs", significance is tested within Danish pig samples from 2020.<br> * rab.all: median clr value for all samples in the feature<br> * rab.win.conditionA: median clr value for the condition A of samples<br> * rab.win.conditionB: median clr value for the condition B of samples<br> * diff.btw: median difference in clr values between A and B conditions<br> * diff.win: median of the largest difference in clr values within A and B conditions<br> * effect : median effect size: diff.btw / max(diff.win) for all instances<br> * overlap : proportion of effect size that overlaps 0 (i.e. no effect)<br> * we.ep: Expected P value of Welch’s t test<br> * we.eBH: Expected Benjamini-Hochberg corrected P value of Welch’s t test<br> * wi.ep: Expected P value of Wilcoxon rank test<br> * wi.eBH: Expected Benjamini-Hochberg corrected P value of Wilcoxon test<br> * parts: gene name<br> * conditionA: label of condition A that is compared against condition B<br> * conditionB: label of condition B that is compared against condition A<br> * conditions.A.vs.B: label to explain condition A compared against condition B<br> NOTE: see for more explanation of the output of ALDEx2 https://www.bioconductor.org/packages/release/bioc/vignettes/ALDEx2/inst/doc/ALDEx2_vignette.html#5_ALDEx2_outputs SD5: Multi-VCF file containing SNP information on mcr alleles. Can be used to construct consensus sequences. SD6: FASTA file containing all unique consensus sequences reported in the manuscript. SD7: CSV file with an overview of which metagenome contains which unique consensus sequence.