Table 2:

Flags and parameters used in INFO field of VCF files in various HapMap 3 versions

Parameter	3.1.1	3.2.1 unimp	3.2.1 imp	Description
DP	+	+	+	Total read depth at the site
NZ	+	+	+	Number of taxa with called genotypes
AD	+	+	+	Allelic depths (reference, alternative in order listed in ALT field)
AC	+	+	+	Numbers of alternative alleles in order listed in ALT field
AQ	+	+	+	Average allele base qualities (reference, alternative in order listed in ALT field) computed in HapMap 3.1.1 from 916 taxa
GN	+	+	+	Numbers of genotypes (AA,AB,BB or AA,AB,AC,BB,BC,CC if 2 alt alleles present)
HT	+	+	+	Number of heterozygotes
EF	+	+	+	EF = het_frequency/(presence_frequency*minor_allele_frequency); computed in HapMap 3.1.1 from 916 taxa
PV	+	+	+	P-value from segregation test, computed in HapMap 3.1.1 from 916 taxa
MAF	+	+	+	Minor allele frequency (summed up over all alternative alleles)
MAF0	-	-	+	Minor allele frequency in unimputed HapMap 3.2.1
FH	+	-	-	Fraction of heterozygous taxa among the 506 taxa with more than 50% nonmissing genotypes on chr 10
FH2	+			Site with FH greater than 2%
IBD1	+	+	+	Only 1 allele present in IBD contrasts—based on 916 taxa of HapMap 3.1.1
LLD	+	+	+	Site in local LD with GBS map—based on 916 taxa of HapMap 3.1.1
NI5	+	+	+	Indel or site within 5 bp of a putative indel—from 916 taxa of HapMap 3.1.1
INHMP311	-	+	+	Site present in HapMap 3.1.1
ImpHomoAccuracy	-	-	+	Fraction of homozygotes imputed back into homozygotes
ImpMinorAccuracy	-	-	+	Fraction of minor allele homozygotes imputed back into minor allele homozygotes
DUP	-	-	+	Site with heterozygote frequency >3%—based on unimputed HapMap 3.2.1 genotypes

“+” and “-” indicate presence or absence, respectively, of a parameter or flag in a given version of HapMap. For example, “-++” means the parameter is present in the VCF file of both unimputed and imputed HapMap 3.2.1, and absent from HapMap 3.1.1. VCF files: Unless indicated otherwise, all parameters are computed from depths and genotypes in the current VCF file.