How to determine LOD threshold for qtl analysis if permutation LOD score are all bigger than the scanone lod score?

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R

#Permutation test

    operm10 <- scanone(boltbdh23_SPAD,method = "em",n.perm=1000,verbose = TRUE)
    summary(operm10)

> summary(operm10)
LOD thresholds (1000 permutations)
    lod 
5% 3.05 
10% 2.69
#Looking for qtls 
#scanone em method 

    out1.em1<-scanone(boltbdh23_SPAD,method = "em")
    plot(out1.em1, main=" EM SPAD",ylim=c(0,2),alternate.chrid = TRUE)
    summary(out1.em1)#single largest from each chromosome

`summary(out1.em1)`#single largest from each chromosome
              chr pos lod 
SC1_42581169 C1 96.5 0.449
SC2_5981392 C2 77.4 0.849
cC3.loc70 C3 70.0 1.768
SC4_52892339 C4 143.6 0.705
SC5_18771319 C5 136.1 0.409
SC6_7166279 C6 21.3 1.594
SC7_20481375 C7 21.8 0.486
SC8_39579611 C8 130.9 0.523
SC9_11060404 C9 160.8 1.614

    max(out1.em1)

> max(out1.em1)

          chr pos lod

cC3.loc70 C3 70 1.77`

As we know we need genome wide LOD threshold to determine the significant qtls but the 5% LOD value (here. 3.05) i am getting is way bigger than any other LOD score I am getting for every chromosome and maximum value (1.77). Help me how to correct this and what I am doing wrong.

What I have tried:

#Permutation test
operm1000 <- scanone(boltbdh23_shoot_Dwt,n.perm=1000,verbose = TRUE) #with 1000 permutation 
plot(operm1000)
summary(operm1000)
summary(operm1000,alpha=c(0.05,0.10,0.20,0.30,0.40,0.50,0.60,0.70,0.80,0.90))


#Looking for qtls
#scanone em method
out1.em1<-scanone(boltbdh23_shoot_Dwt,method = "em")
plot(out1.em1, main=" EM LOD Fwt",ylim=c(0,2),alternate.chrid = TRUE)
summary(out1.em1)#single largest from each chromosome
max(out1.em1)