Table of Changes
----------------

Uploaded variation      	[VEP output - ignore]
Chrom                   	Chromosome
Pos                     	Position
Allele                  	[VEP output - ignore]
Gene                    	Gene in Ensembl format (ENSG)
Feature                 	Transcript in Ensembl format (ENST) or Regulatory region in Ensembl format (ENSR)
Feature_type            	Type of feature (Transcript or RegulatoryFeature)
Consequence             	Consequence of change (NonSyn, regulatory motif, 3'UTR, etc.)
cDNA_position           	Position in cDNA
CDS_position            	Position in CDS
Protein_position        	Position in protein
Amino_acids             	Change in amino acid (reference / alternative)
Codons                  	Change in codons (reference / alternative)
Existing_variation      	[VEP output - ignore]
Extra                   	Structural consequences (PolyPhen, SIFT, Condel)
Human                   	Fixed derived or high-frequency derived allele (>0.9) in humans ("1" if no db SNP exits; "1.0" if 1000G ancestral global frequency is 0)
Archaics_(Vindija,Sidron,AltaiNea,Denisova)	Alleles for Vindija exome, Sidron exome, Altai Neandertal and Denisova
Ancestor			Human-Chimp ancestor allele (EPO)
Gorilla				Human-Gorilla ancestor allele (EPO)
Orangutan			Human-Orangutan ancestor allele (EPO)
States				Allele states for Vindija exome, Sidron exome, Altai Neandertal and Denisova (A = ancestral, H = derived like human majority allele, N = derived different from human majority allele
dbSNP				dbSNP ID
Human_1000G(Global)		Global human ancestral frequency based on 1000G data
Flag				CpG if in CpG island; RM if in repeat masked region; LowQual if conflicting GATK calls; SysErr if prone to systematic errors; InDelNear if indels nearby
GERP_score			GERP score
Mammal_score			Mammal conservation score (excluding humans)
Primate_score			Primate conservation score (excluding humans)
B_score				B-score
Mappability_score		Mappability score
VCF_info			INFO fields from GATK VCF file
VCF_format			Format field information taken from GATK VCF file
VCF_values			Read information taken from GATK VCF file
Strand				+ or -, only relevant to genic sites