PGDSpider population defintion is different in output file

Question

[qwzhang0601]

Hi all:

I am using PGDSplider to tranfer VCF files into "structure" format (used as input of the tool faststructure for population structure analysis). I included the population definition like below. Briefly, I have 26 populations from 1000 genome project. The output file also grouped the individuals into 26 populations, but the population number is different from those that I defined. For example "HG00154" was assigned population number 1. Do anyone know why this happen? Thanks

HG00154 14 HG00155 14 HG00157 14 HG00158 14 HG00159 14 HG00160 14 HG00171 13 HG00173 13 HG00174 13 HG00176 13 HG00177 13