Column Name: Description

SNP: SNPs contained within the 160nt sequence segment.
hap: Haplotype encoded in this sequence segment.  0s and 1s correspond to reference and alternate alleles; mutated_ARE, mutated_CDE, etc. correspond to deliberate mutations
ids: A name for the sequence segment.
overlapWith: Gives a list of elements the sequence segment overlaps with.
overlapWithAndSNPInside: Gives a list of elements the sequence segment overlaps with and which a SNP in the oligo overlaps.
region: Takes the form GENE|CHROM:START-END.
seq: The sequence of the segment.
iscontrol: 1 if reference; 0 if a deliberate mutation or alt allele
parent_control_oligo: The id of the reference segment for a deliberate mutation or alt allele (its own id if it is a reference).
issnp: 1 if it is a SNP, 0 otherwise
GC_content: Fraction of GC.
ratios_T0: RNA/(RNA+DNA) at T0 for the sequence segment (summing over all clones for RNA and DNA)
ratios_T4T0: ratios_T4/(ratios_T4+ratios_T0)
ratios_T0_GC_resid: ratios_T0 after residualizing with respect to GC (better to use this)
ratios_T4T0_GC_resid: ratios_T4T0 after residualizing with respect to GC (better to use this)
effect_size_T0: Difference in ratios_T0 between reference and alt/mutant (sign is alt/mutant minus reference)
effect_size_T4T0: Difference in ratios_T4T0 between reference and alt/mutant (sign is alt/mutant minus reference)
effect_size_T0_GC_resid: effect_size_T0 after residualizing by GC (better to use this but difference is small)
effect_size_T4T0_GC_resid: effect_size_T4T0 after residualizing by GC (better to use this but difference is small)
one_ARE_deleted: 1 if exactly 1 ARE was deliberately mutated, 0 otherwise
top_ARE_deleted: 1 if the mutated ARE was the longest ARE in the sequence segment, 0 otherwise
motif_AREs_numbered_BakheetPlus: ARED-Plus "cluster" number.  -1 if no ARE, 0 if ARE smaller than ARED-Plus clusters but larger than "AUUUA".
ARE_registration_perfect: Registration of the ARE, assuming perfect match to AUUUA motif with no mismatches (integer value, nan if no ARE present).
ARE_length_perfect: Length of the ARE, assuming perfect match to AUUUA motif with no mismatches (integer value, nan if no ARE present).
CDE_stem_lengths: Length of the lower CDE stem.  -1 means no CDE; 0 (or 1) means there is no lower stem but the motif exists.
parent_CDE_stem_length: If hap=='mutated_CDE', this is the length of the lower CDE stem of the parent (corresponding un-mutated) sequence.
ratios_T2T0: ratios_T2/(ratios_T2+ratios_T0)
ratios_T2T0_GC_resid: ratios_T2T0 after residualizing with respect to GC (better to use this)
effect_size_T2T0: Difference in ratios_T2T0 between reference and alt/mutant (sign is alt/mutant minus reference)
effect_size_T2T0_GC_resid: effect_size_T2T0 after residualizing by GC (better to use this but difference is small)
ratios_T6T0: ratios_T6/(ratios_T6+ratios_T0)
ratios_T6T0_GC_resid: ratios_T6T0 after residualizing with respect to GC (better to use this)
effect_size_T6T0: Difference in ratios_T6T0 between reference and alt/mutant (sign is alt/mutant minus reference)
effect_size_T6T0_GC_resid: effect_size_T6T0 after residualizing by GC (better to use this but difference is small)
parent_motif_AREs_numbered_BakheetPlus: For mutated AREs, this is the ARED-Plus "cluster" number of the "parent" ARE.