To elaborate on the title...

After filtering from 19,578 to 2209 binary SNPs, I converted the genlight object into a structure format to be used for fastSTRUCTURE in the LEA package. I noticed when running a cross-entropy test that it increases to 5372 loci. (Side note, the species I am studying is an aquarium fish so there is a lot of genetic inbreeding, the reason for such low SNPs)

Is this normal when running this analysis? I am attaching my script below. I would greatly appreciate any help!

glxh<-gl.read.dart(filename=" NoMolly",covfilename="metadataallnomolly.csv")

save(glxh, file="xhell.rdata") load("xhell.rdata")

gl.report.monomorphs(glxh)

glxh1 <- gl.filter.monomorphs(glxh)

gl.report.callrate(glxh1, method = "loc")

glxh2 <- gl.filter.callrate(glxh1, method = "loc", threshold= 0.82)

glxh3 <- gl.filter.secondaries(glxh2)

gl2faststructure(glxh3, outfile = "glxh3.str", probar = TRUE)

struct2geno("glxh3.str", ploidy = 2, FORMAT = 2)

project = snmf("glxh3.geno", K = 1:20, entropy = TRUE, repetitions = 10, project = "new")