This directory contains the output from your MetaQuery search
If you use any of these results, please cite:
Nayfach, S., Fischbach, M.A, and Pollard, K.S. MetaQuery: a webserver for rapid annotation and quantitative analysis of genes in the human gut microbiome. (In preparation).

This data is organized into the following 4 sub-directories:
/in
/out
/analyses
/plots

in
--------------
parameters.txt
	-parameters specified in web form
query.fa
	-uploaded query sequence(s)

out
--------------
abundance.matrix
	-gene abundances for 1,267 samples
percent_id.matrix
	-abundance-weighted percent identities (between query and reference) for 1,267 samples
	-high values indicates the presence of mostly close homologs
	-lower values indicate the presence of mostly remote homologs
	
analyses
--------------
gene_summary.table
	-summary statistics for gene abundance and %ID across 1,267 samples
	-mean: mean abundance/%ID
	-min: maximum abundance/%ID
	-max: maximum abundance/%ID
	-cv: coefficient of variation of abundance/%ID

gene_covariation.matrix
	-Spearman correlation matrix

ags_covariation.table
	-Spearman correlations of average genome size versus gene abundance
	-Average genome size estimates were obtained using MicrobeCensus
	
taxonomic_assoc.table
	-Spearman correlations of taxonomic abundances size versus gene abundance
	-taxonomic abundances were obtained using MetaPhlan

continent_assoc.table
	-comparison of gene abundance between healthy individuals from different continents
	-description of groups:
		-North America: samples from the HMP study
		-Europe: samples from the MetaHIT, MGS, IGC, and Richness studies
		-China: samples from the T2D study
		-Samples with IBD or Diabetes were exlcuded
	-fields 2-4 indicate median gene abundance within each group
	-field 5-6 indicate the p-value and q-value from a Kruskal-Wallis test
	-the Benjamini-Hochberg method was used for multiple testing correction

diabetes_assoc.table
	-comparison of gene abundance between healthy controls and individuals with diabetes
	-description of groups:
		-All samples are from Chinese individuals from the T2D study
	-fields 2-3 indicate median gene abundance within each group
	-field 4-5 indicate the p-value and q-value from a Kruskal-Wallis test
	-the Benjamini-Hochberg method was used for multiple testing correction
	
diabetes_assoc.table
	-comparison of gene abundance between healthy controls, individuals with crohn's disease, and individuals with ulcerative colitis
	-description of groups:
		-All samples are from Spanish individuals from the MetaHIT and Richness studies
	-fields 2-4 indicate median gene abundance within each group
	-field 5-6 indicate the p-value and q-value from a Kruskal-Wallis test
	-the Benjamini-Hochberg method was used for multiple testing correction


plots
--------------
abundance_pid
	-directory containing plots that correspond to gene_summary.table
	-plots are available only for the first 1000 genes
continents, diabetes, ibd
	-directories containing boxplots that correspond to statistical analyses
	-plots are available only for the first 1000 genes
ags
	-average genome size versus gene abundance
	-plots are available only for the first 1000 genes
covariation
	-Matrix of spearman correlations for all pairs of query genes