dbPSHP precomputed dataset are compressed by bgzip and indexed by tabix, which can be downloaded in our FTP server. Please use tabix to query the local file!

All of selection signals are encapsulated into VCF INFO field and the primary items are listed in the following table, please also check the descriptions from VCF HEAD for latest information:

Table 1: The scope and calculated scores in the dbPSHP

Attribute

Evaluation Term

Abbr.

variant genotype properties

derived allele

DA

ancestral allele

AA

allele frequency

DAF

AAF

genotype frequency

GFHOM1

GFHET

GFHOM2

Hardy-Weinberg equilibrium

HWE1

HWE2

variant heterozygosity

heterozygosity

HET

nucleotide diversity

PI

within population diversity

Tajima's D

TD

long-range haplotypes

integrated extended haplotype homozygosity

IHH

integrated haplotype score

UIHS

IHS

differentiation between populations

difference of derived allele frequency

DDAF

DDAF_POP1_POP2

fixation index

FST1

FST1_POP1_POP2

FST2

FST2_POP1_POP2

cross-population extended haplotype homozygosity

UXPEHH

XPEHH_POP1_POP2

cross-population composite likelihood ratio

XPCLR

XPCLR_POP1_POP2

evolutionary conservation

neutral rate

NR

rejected substitution

RS

DAF is the allele frequency for derived allele; AAF is the allele frequency for ancestral allele; GFHOM1 is the genotype frequency for homozygous AA; GFHET is the genotype frequency for heterozygous Aa; GFHOM2 is the genotype frequency for homozygous aa; HWE1 is the value of simple chi square goodness-of-fit test; HWE2 is the p-value of exact test; FST1 is the FST of Wright's approximate formula; FST2 is the FST of Cockerham & Weir estimator; UIHS is the unstandardized integrated haplotype score; UXPEHH is the unstandardized cross-population extended haplotype homozygosity; POP1_POP2 represent the pairwise scores of two specific populations.

 

 

 

 

If you are using these dataset, please cite the website if possible.
dbPSHP: a database of recent positive selection across human populations http://jjwanglab.org/dbpshp



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