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:
* 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.
* rab.all:  median clr value for all samples in the feature
* rab.win.conditionA:  median clr value for the condition A of samples
* rab.win.conditionB: median clr value for the condition B of samples
* diff.btw: median difference in clr values between A and B conditions
* diff.win: median of the largest difference in clr values within A and B conditions
* effect : median effect size: diff.btw / max(diff.win) for all instances
* overlap : proportion of effect size that overlaps 0 (i.e. no effect)
* we.ep: Expected P value of Welch’s t test
* we.eBH: Expected Benjamini-Hochberg corrected P value of Welch’s t test
* wi.ep: Expected P value of Wilcoxon rank test
* wi.eBH: Expected Benjamini-Hochberg corrected P value of Wilcoxon test
* parts: gene name
* conditionA: label of condition A that is compared against condition B
* conditionB: label of condition B that is compared against condition A
* conditions.A.vs.B: label to explain condition A compared against condition B
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.