table mpra_variant
"BED6+10 MPRA variant level common file format"
(
string chrom; "Reference sequence chromosome or scaffold"
uint chromStart; "Start position of the variant in chromosome, 0-based inclusive"
uint chromEnd; "End position of the variant in chromosome, 0-based exclusive"
string name; "Name of tested variant"
uint score; "Indicates how dark the peak will be displayed in the browser (0-1000)"
char[1] strand; "+ or - for strand the variant was tested in, . for unknown"
float log2FoldChange; "Fold change (alt output/input ratio divided by ref output/input ratio , in log2 space)"
float inputCountRef; "Input count reference allele, normalized (CPM), mean across replicates"
float outputCountRef; "Output count reference allele, normalized (CPM), mean across replicates"
float inputCountAlt; "Input count alternative allele, normalized (CPM), mean across replicates"
float outputCountAlt; "Output count alternative allele, normalized (CPM), mean across replicates"
float minusLog10PValue; "-log10 of P-value"
float minusLog10QValue; "-log10 of Q-value (FDR)"
float postProbEffect; "Posterior probability of a regulatory effect"
float CI_lower_95; "Lower bound of a 95% interval for the variant effect"
float CI_upper_95; "Upper bound of a 95% interval for the variant effect"
uint variantPos; "0-based position of the start of the variant in the tested sequence, -1 if aggregated effect over multiple positions"
string refAllele; "normalized Canonical SPDI reference variant sequence, allowed chars [A,T,G,C]"
string altAllele; "normalized Canonical SPDI alternative variant sequence, allowed chars [A,T,G,C]"
)
