library(dartRverse)
library(tidyverse)
library(RColorBrewer)
library(patchwork)
library(scales)
library(ggplot2)
library(gridExtra)
library(grid)
library(raster)
library(otuSummary) 13 Combining Genomic Resources
Session Presenters
Introduction
Chromosomal rearrangements are often associated with local adaptation and speciation because they suppress recombination, and as a result, rearrangements have been implicated in disrupting geneflow. Although there is strong evidence to suggest that chromosome rearrangements are a factor in genetic isolation of divergent populations, the underlying mechanism remains elusive. Here we applied an integrative cytogenetics and genomics approach testing whether chromosomal rearrangements are the initial process, or a consequence, of population divergence in the dwarf goanna, Varanus acanthurus. Specifically, we tested whether chromosome rearrangements are indicators of genetic barriers that can be used to identify divergent populations by looking at geneflow within and between populations with rearrangements. We found that geneflow was present between individuals with chromosome rearrangements within populations, but there was no geneflow between populations that had similar chromosome rearrangements. Moreover, we identified a correlation between reduced genetic variation in populations with a higher frequency of homozygous submetacentric individuals. These findings suggest that chromosomal rearrangements were widespread prior to divergence and because we found populations with higher frequencies of submetacentric chromosomes were associated with lower genetic diversity, this could indicate that polymorphisms within populations are early indicators of genetic drift.
Required packages
make sure you have the packages installed, see Install dartRverse
Geneflow between Karyotypes
# setup -----------------------
## load ---
vac.glch2 <- readRDS("./data/spiny_gl1.rds")
# missing karyotype MM in East population
vac.glch2@other$ind.metrics$karyo[grep("AA095619", vac.glch2@ind.names)] <- "MM"
## overview --------------------------------------------------------------------
vac.glch2 /// GENLIGHT OBJECT /////////
// 233 genotypes, 301,738 binary SNPs, size: 302 Mb
19405083 (27.6 %) missing data
// Basic content
@gen: list of 233 SNPbin
@ploidy: ploidy of each individual (range: 2-2)
// Optional content
@ind.names: 233 individual labels
@loc.names: 301738 locus labels
@loc.all: 301738 alleles
@pop: population of each individual (group size range: 1-36)
@other: a list containing: loc.metrics ind.metrics latlon loc.metrics.flags history verbose pop(vac.glch2) %>% table.
b baritji bb c cbb dr dw ea East ekim
4 15 1 1 15 1 4 5 10 4
gd kim mi nb North q rg sd South storri
3 30 4 1 9 1 9 8 9 5
vd wa wam West wm
3 36 32 21 2 table(vac.glch2@other$ind.metrics$PCR1)
f m
172 23 38 vac.glch2@other$ind.metrics$sex = NULL
sex = toupper(as.character(vac.glch2@other$ind.metrics$PCR1))
# sex[sex==""] = "M" #TODO FIX na
vac.glch2@other$ind.metrics$sex <- sex
#gl.smearplot(vac.glch2, group.pop = FALSE)
## filtering -------------------------------------------------------------------
vac.pops <-gl.keep.pop(vac.glch2, pop.list = c("North","South","East","West"))Starting gl.keep.pop
Processing genlight object with SNP data
Checking for presence of nominated populations
Retaining only populations North, South, East, West
Warning: Resultant dataset may contain monomorphic loci
Locus metrics not recalculated
Completed: gl.keep.pop #gl.smearplot(vac.pops, group.pop = TRUE)sex <- gl.filter.sexlinked(vac.glch2, system = "zw")
table(sex$w.linked@other$loc.metrics$Chrom_Varanus_JD_infer_w)
scaf_10323 scaf_1064 scaf_1092 scaf_1121 scaf_11303 scaf_1133
299862 2 14 3 19 1 1
scaf_13939 scaf_14539 scaf_15833 scaf_159 scaf_164 scaf_16462 scaf_16941
5 5 1 12 28 1 6
scaf_17264 scaf_17378 scaf_175 scaf_17533 scaf_176 scaf_1768 scaf_177
2 3 63 2 28 4 17
scaf_17745 scaf_181 scaf_18976 scaf_19496 scaf_19546 scaf_19676 scaf_19678
1 23 7 5 12 1 15
scaf_19686 scaf_19710 scaf_20029 scaf_20122 scaf_20137 scaf_20324 scaf_2063
1 6 20 3 1 9 1
scaf_2296 scaf_24228 scaf_2674 scaf_2686 scaf_28831 scaf_29153 scaf_29340
1 3 4 2 9 1 7
scaf_30879 scaf_31396 scaf_32040 scaf_33358 scaf_33490 scaf_33621 scaf_33754
3 4 3 4 4 3 9
scaf_33755 scaf_33815 scaf_33834 scaf_33937 scaf_33995 scaf_34187 scaf_34257
10 6 3 5 3 1 5
scaf_34264 scaf_34293 scaf_34296 scaf_34780 scaf_35217 scaf_37485 scaf_37914
3 59 13 1 2 34 4
scaf_38564 scaf_39169 scaf_39480 scaf_39564 scaf_39585 scaf_39615 scaf_40621
10 29 1 4 4 1 1
scaf_40908 scaf_40937 scaf_41277 scaf_41356 scaf_41363 scaf_41402 scaf_4141
2 8 9 1 11 17 6
scaf_41492 scaf_41662 scaf_42222 scaf_42472 scaf_42597 scaf_42603 scaf_42605
25 6 1 16 9 18 8
scaf_42608 scaf_42630 scaf_43039 scaf_43122 scaf_43126 scaf_43132 scaf_43207
13 47 15 3 32 5 39
scaf_43209 scaf_43227 scaf_43364 scaf_43405 scaf_43511 scaf_43848 scaf_43901
13 7 20 16 3 2 14
scaf_43906 scaf_43915 scaf_43977 scaf_44080 scaf_44104 scaf_44191 scaf_44251
19 53 89 70 91 2 1
scaf_44262 scaf_44332 scaf_44349 scaf_44350 scaf_44435 scaf_44535 scaf_44569
75 8 8 30 13 52 8
scaf_591 scaf_619 scaf_6829 scaf_7848 scaf_8162 scaf_8185 scaf_9006
33 25 1 21 3 5 6
scaf_9015 scaf_9025 scaf_9028 scaf_9029 scaf_9033 scaf_9043 scaf_939
6 5 22 1 1 2 45
scaf_10851 scaf_11034 scaf_18166 scaf_20103 scaf_22094 scaf_2413 scaf_30511
2 4 1 2 2 6 2
scaf_33868 scaf_33956 scaf_34282 scaf_39568 scaf_40828 scaf_41352 scaf_41577
2 2 3 2 4 5 6
scaf_42194 scaf_42206 scaf_42407 scaf_42590 scaf_43134 scaf_43255 scaf_43347
8 2 1 2 11 1 1
scaf_835 scaf_9036 scaf_9133 scaf_944 scaf_1049 scaf_10750 scaf_10952
2 6 8 4 3 1 2
scaf_14926 scaf_16087 scaf_16565 scaf_17565 scaf_18106 scaf_18615 scaf_19081
2 1 5 2 4 1 1
scaf_19305 scaf_19657 scaf_19658 scaf_19659 scaf_19794 scaf_19885 scaf_20048
1 1 1 1 1 3 3
scaf_20059 scaf_20116 scaf_20213 scaf_20222 scaf_20326 scaf_23061 scaf_2445
2 1 1 1 1 2 1
scaf_2667 scaf_28826 scaf_29810 scaf_30302 scaf_32488 scaf_32653 scaf_32815
1 1 3 2 2 1 1
scaf_33422 scaf_33451 scaf_33595 scaf_33665 scaf_33841 scaf_33845 scaf_34167
2 3 1 2 1 10 1
scaf_34261 scaf_34265 scaf_34360 scaf_35141 scaf_37830 scaf_37837 scaf_37982
1 2 2 1 1 1 1
scaf_38014 scaf_38163 scaf_38481 scaf_39075 scaf_39298 scaf_39668 scaf_39916
1 1 1 1 1 5 4
scaf_40887 scaf_41264 scaf_41274 scaf_41390 scaf_4168 scaf_41789 scaf_42039
4 4 5 1 1 4 3
scaf_42444 scaf_42617 scaf_43226 scaf_43673 scaf_44264 scaf_44620 scaf_44621
2 1 1 1 2 1 2
scaf_4750 scaf_4773 scaf_526 scaf_574 scaf_8262 scaf_8885 scaf_8931
3 1 1 1 3 3 3
scaf_8974 scaf_901 scaf_9081 scaf_950
1 1 1 2 ## start ----------
vac.gl1 <- gl.filter.callrate(vac.pops, method = "loc", threshold = 0.80)Starting gl.filter.callrate
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Warning: Data may include monomorphic loci in call rate
calculations for filtering
Recalculating Call Rate
Removing loci based on Call Rate, threshold = 0.8 
Completed: gl.filter.callrate vac.gl1 <- gl.filter.callrate(vac.gl1, method = "ind", threshold = 0.75) Starting gl.filter.callrate
Processing genlight object with SNP data
Warning: Data may include monomorphic loci in call rate
calculations for filtering
Recalculating Call Rate
Removing individuals based on Call Rate, threshold = 0.75 
Note: Locus metrics not recalculated
Note: Resultant monomorphic loci not deleted
Completed: gl.filter.callrate vac.gl1 <- gl.filter.reproducibility(vac.gl1, t = 0.99)Starting gl.filter.reproducibility
Processing genlight object with SNP data
Removing loci with repeatability less than 0.99 
Completed: gl.filter.reproducibility vac.gl1 <- gl.filter.monomorphs(vac.gl1, v = 0)
## colours -----------------------------------
popcolors <- c(East = "#0571b0", North = "#404040",
South = "#5e3c99", West = "#e66101")
karyocolors <- c("MM" = "red", "MA" = "black", "AA" = "blue")## pcoa ------------------------------------------------------------------------
pc <- gl.pcoa(vac.gl1, nfactors = 5)Starting gl.pcoa
Processing genlight object with SNP data
Performing a PCA, individuals as entities, loci as attributes, SNP genotype as state
Starting gl.colors
Selected color type 2
Completed: gl.colors 
Completed: gl.pcoa ## ibd data --------------------------------------------------------------------
# pop
indexXY <- complete.cases(vac.gl1@other$latlon) # missing locations
vac.gl17 <- gl.keep.ind(vac.gl1,ind.list = indNames(vac.gl1)[indexXY])Starting gl.keep.ind
Processing genlight object with SNP data
Deleting all but the listed individuals ABTC11930_aca, ABTC11932_aca, ABTC72881_aca, ABTC8929_aca, ABTC8938_aca, AA095616, AA093614, AA095550, AA095620, AA095553, AA095548, AA095617, AA093615, AA095626, AA095636, AA095546, AA096028, AA095562, AA095623, AA095635, AA095547, AA096030, AA095629, AA095624, AA095637, AA095545, AA095568, AA095625, AA095542, AA095570, AA095549, AA095551, AA095543, AA096029, AA095627, AA095540, AA095544, AA095634, AA095569, AA095539a
Warning: Resultant dataset may contain monomorphic loci
Locus metrics not recalculated
Completed: gl.keep.ind latAdjust <- runif(nInd(vac.gl17))/10000 # unique individual locations
vac.gl17@other$latlon$lat <- vac.gl17@other$latlon$lat+ latAdjust
# karyo
vac.gl18 <- gl.drop.pop(vac.gl17, as.pop = "karyo", pop.list = "")Starting gl.drop.pop
Processing genlight object with SNP data
Temporarily assigning karyo as population
Checking for presence of nominated populations, deleting them
Warning: Resultant dataset may contain monomorphic loci
Locus metrics not recalculated
Restoring population assignments to initial state
Completed: gl.drop.pop pop(vac.gl18) <- vac.gl18@other$ind.metrics$karyo
# figure 3 ---------------------------------------------------------------------
popi <- levels(vac.gl1@pop)
vac.edit <- vac.gl1
# all East population assumed to be MM
vac.edit@other$ind.metrics$karyo[pop(vac.gl1)=="East"] <- "MM"Within population PCoA and IBD
for(i in 1:4){
#pcoa
vac.popi <- gl.keep.pop(vac.edit, pop.list = popi[i], as.pop = "pop")
vacp <- gl.filter.monomorphs(vac.popi, verbose = 0)
pop(vacp) <- vacp@other$ind.metrics$karyo
vacpK <- gl.keep.pop(vacp, as.pop = "karyo", pop.list = names(karyocolors), verbose = 0)
pca <- gl.pcoa(vacpK, nfactors = 5)
gl.pcoa.plot(pca, vacpK)#plot.pcoa(pca, vacpK, xpc = 1, ypc = 2, popColors = karyocolors)
plotfiles <- list.files(tempdir())[grep("Plot", list.files(tempdir()))]
unlink(paste0(tempdir(), "/", plotfiles))
#ibd
gl.ibd(vacpK, distance = "propShared", paircols = "pop",
Dgeo_trans = "Dgeo")
}Starting gl.keep.pop
Processing genlight object with SNP data
Temporarily assigning pop as population
Checking for presence of nominated populations
Retaining only populations East
Locus metrics not recalculated
Resetting population assignments to initial state
Completed: gl.keep.pop
Warning: Listed population MA not present in the dataset -- ignored
Warning: Listed population AA not present in the dataset -- ignored
Starting gl.pcoa
Processing genlight object with SNP data
Performing a PCA, individuals as entities, loci as attributes, SNP genotype as state
Starting gl.colors
Selected color type 2
Completed: gl.colors 
Completed: gl.pcoa
Starting gl.pcoa.plot
Processing an ordination file (glPca)
Processing genlight object with SNP data
Plotting populations in a space defined by the SNPs
Preparing plot .... please wait
Completed: gl.pcoa.plot
Starting gl.ibd
Analysis performed on the genlight object.
Coordinates transformed to Mercator (google) projection to calculate distances in meters.Warning: Removed 9 rows containing non-finite outside the scale range
(`stat_smooth()`).Warning: Removed 9 rows containing missing values or values outside the scale range
(`geom_point()`).
Removed 9 rows containing missing values or values outside the scale range
(`geom_point()`).
Removed 9 rows containing missing values or values outside the scale range
(`geom_point()`).
Coordinates used from: x@other$latlon (Mercator transformed)
Transformation of Dgeo: Dgeo
Genetic distance: propShared
Tranformation of Dgen: Dgen
Mantel statistic based on Pearson's product-moment correlation
Call:
vegan::mantel(xdis = Dgen, ydis = Dgeo, permutations = permutations, na.rm = TRUE)
Mantel statistic r: 0.6174
Significance: 0.003
Upper quantiles of permutations (null model):
90% 95% 97.5% 99%
0.290 0.372 0.431 0.507
Permutation: free
Number of permutations: 999
Completed: gl.ibd
Starting gl.keep.pop
Processing genlight object with SNP data
Temporarily assigning pop as population
Checking for presence of nominated populations
Retaining only populations North
Locus metrics not recalculated
Resetting population assignments to initial state
Completed: gl.keep.pop
Warning: Listed population MM not present in the dataset -- ignored
Starting gl.pcoa
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Performing a PCA, individuals as entities, loci as attributes, SNP genotype as state
Starting gl.colors
Selected color type 2
Completed: gl.colors 
Completed: gl.pcoa
Starting gl.pcoa.plot
Processing an ordination file (glPca)
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Plotting populations in a space defined by the SNPs
Preparing plot .... please wait
Completed: gl.pcoa.plot
Starting gl.ibd
Analysis performed on the genlight object.
Coordinates transformed to Mercator (google) projection to calculate distances in meters.
Coordinates used from: x@other$latlon (Mercator transformed)
Transformation of Dgeo: Dgeo
Genetic distance: propShared
Tranformation of Dgen: Dgen
Mantel statistic based on Pearson's product-moment correlation
Call:
vegan::mantel(xdis = Dgen, ydis = Dgeo, permutations = permutations, na.rm = TRUE)
Mantel statistic r: 0.3604
Significance: 0.025
Upper quantiles of permutations (null model):
90% 95% 97.5% 99%
0.214 0.286 0.353 0.411
Permutation: free
Number of permutations: 999
Completed: gl.ibd
Starting gl.keep.pop
Processing genlight object with SNP data
Temporarily assigning pop as population
Checking for presence of nominated populations
Retaining only populations South
Locus metrics not recalculated
Resetting population assignments to initial state
Completed: gl.keep.pop
Warning: Listed population AA not present in the dataset -- ignored
Starting gl.pcoa
Processing genlight object with SNP data
Performing a PCA, individuals as entities, loci as attributes, SNP genotype as state
Starting gl.colors
Selected color type 2
Completed: gl.colors 
Completed: gl.pcoa
Starting gl.pcoa.plot
Processing an ordination file (glPca)
Processing genlight object with SNP data
Plotting populations in a space defined by the SNPs
Preparing plot .... please wait
Completed: gl.pcoa.plot
Starting gl.ibd
Analysis performed on the genlight object.
Coordinates transformed to Mercator (google) projection to calculate distances in meters.
Coordinates used from: x@other$latlon (Mercator transformed)
Transformation of Dgeo: Dgeo
Genetic distance: propShared
Tranformation of Dgen: Dgen
Mantel statistic based on Pearson's product-moment correlation
Call:
vegan::mantel(xdis = Dgen, ydis = Dgeo, permutations = permutations, na.rm = TRUE)
Mantel statistic r: 0.643
Significance: 0.003
Upper quantiles of permutations (null model):
90% 95% 97.5% 99%
0.307 0.376 0.637 0.643
Permutation: free
Number of permutations: 999
Completed: gl.ibd
Starting gl.keep.pop
Processing genlight object with SNP data
Temporarily assigning pop as population
Checking for presence of nominated populations
Retaining only populations West
Locus metrics not recalculated
Resetting population assignments to initial state
Completed: gl.keep.pop
Starting gl.pcoa
Processing genlight object with SNP data
Performing a PCA, individuals as entities, loci as attributes, SNP genotype as state
Starting gl.colors
Selected color type 2
Completed: gl.colors 
Completed: gl.pcoa
Starting gl.pcoa.plot
Processing an ordination file (glPca)
Processing genlight object with SNP data
Plotting populations in a space defined by the SNPs
Preparing plot .... please wait
Completed: gl.pcoa.plot
Starting gl.ibd
Analysis performed on the genlight object.
Coordinates transformed to Mercator (google) projection to calculate distances in meters.Warning: Removed 36 rows containing non-finite outside the scale range
(`stat_smooth()`).Warning: Removed 36 rows containing missing values or values outside the scale range
(`geom_point()`).
Removed 36 rows containing missing values or values outside the scale range
(`geom_point()`).
Removed 36 rows containing missing values or values outside the scale range
(`geom_point()`).
Coordinates used from: x@other$latlon (Mercator transformed)
Transformation of Dgeo: Dgeo
Genetic distance: propShared
Tranformation of Dgen: Dgen
Mantel statistic based on Pearson's product-moment correlation
Call:
vegan::mantel(xdis = Dgen, ydis = Dgeo, permutations = permutations, na.rm = TRUE)
Mantel statistic r: 0.5041
Significance: 0.014
Upper quantiles of permutations (null model):
90% 95% 97.5% 99%
0.282 0.370 0.431 0.520
Permutation: free
Number of permutations: 999
Completed: gl.ibd Between population PCoA and IBD
# figure 4 ---------------------------------------------------------------------
## pcoa figures ----------------------------------------------------------------
gl.pcoa.plot(pc, vac.gl1, xaxis = 1, yaxis = 2,pt.colors = popcolors)Starting gl.pcoa.plot
Processing an ordination file (glPca)
Processing genlight object with SNP data
Plotting populations in a space defined by the SNPs
Preparing plot .... please wait
Completed: gl.pcoa.plot 
gl.pcoa.plot(pc, vac.gl1, xaxis = 3, yaxis = 4, pt.colors = popcolors)Starting gl.pcoa.plot
Processing an ordination file (glPca)
Processing genlight object with SNP data
Plotting populations in a space defined by the SNPs
Preparing plot .... please wait
Completed: gl.pcoa.plot 
## ibd figures -----------------------------------------------------------------
# pop
gl.ibd(vac.gl17, distance = "propShared",
paircols = "pop", Dgeo_trans = "Dgeo")Starting gl.ibd
Analysis performed on the genlight object.
Coordinates transformed to Mercator (google) projection to calculate distances in meters.
Coordinates used from: x@other$latlon (Mercator transformed)
Transformation of Dgeo: Dgeo
Genetic distance: propShared
Tranformation of Dgen: Dgen
Mantel statistic based on Pearson's product-moment correlation
Call:
vegan::mantel(xdis = Dgen, ydis = Dgeo, permutations = permutations, na.rm = TRUE)
Mantel statistic r: 0.5168
Significance: 0.001
Upper quantiles of permutations (null model):
90% 95% 97.5% 99%
0.0795 0.1093 0.1340 0.1654
Permutation: free
Number of permutations: 999
Completed: gl.ibd $Dgen
ABTC11930_aca ABTC11932_aca ABTC72881_aca ABTC8929_aca
ABTC11932_aca 0.08454080
ABTC72881_aca 0.09019160 0.09276463
ABTC8929_aca 0.09041666 0.09189282 0.09039321
ABTC8938_aca 0.08500393 0.08827010 0.08764128 0.08227897
AA095616 0.14224510 0.14444736 0.13983353 0.14064384
AA093614 0.13119301 0.13448232 0.13044816 0.13082531
AA095550 0.12975810 0.13164186 0.12685137 0.12859441
AA095620 0.09165329 0.09182624 0.09206501 0.08888659
AA095553 0.31563647 0.31520435 0.31885137 0.32395215
AA095548 0.31082402 0.31180427 0.31435175 0.32007863
AA095617 0.14237363 0.14541258 0.14028226 0.14107857
AA093615 0.13113039 0.13273985 0.13040335 0.13007040
AA095626 0.13033422 0.13312409 0.13003856 0.13026280
AA095636 0.09487763 0.09645876 0.09775272 0.09232150
AA095546 0.30893456 0.30981928 0.31402059 0.31772570
AA096028 0.14419338 0.14585513 0.14119674 0.14266633
AA095562 0.12966304 0.13319552 0.12914342 0.13094168
AA095623 0.13126143 0.13356033 0.12987764 0.13087248
AA095635 0.09249621 0.09352207 0.09418239 0.08801618
AA095547 0.30606513 0.30645016 0.31142805 0.31474297
AA096030 0.14322856 0.14503143 0.14134988 0.14173929
AA095629 0.12968866 0.13258012 0.12829711 0.12909769
AA095624 0.12983838 0.13278626 0.12911250 0.13000746
AA095637 0.09294763 0.09432971 0.09540032 0.08963028
AA095545 0.31091314 0.31031033 0.31445160 0.32056864
AA095568 0.12862718 0.13168002 0.12706821 0.12927880
AA095625 0.13053987 0.13229771 0.12933121 0.13076769
AA095542 0.31102069 0.31275665 0.31571472 0.31905866
AA095570 0.14390257 0.14625238 0.14182635 0.14276606
AA095549 0.13034483 0.13305645 0.12854411 0.12953764
AA095551 0.14404059 0.14530848 0.14083547 0.14210848
AA095543 0.31407635 0.31277976 0.31812137 0.32117153
AA096029 0.14515080 0.14674154 0.14195874 0.14332123
AA095627 0.14235573 0.14473684 0.14041481 0.14077953
AA095540 0.13115636 0.13349027 0.13001218 0.13025591
AA095544 0.31095217 0.31076378 0.31572589 0.31948844
AA095634 0.14348749 0.14623684 0.14175393 0.14237073
AA095569 0.13041644 0.13422845 0.12986408 0.13103968
AA095539a 0.31163857 0.31154875 0.31704579 0.31969287
ABTC8938_aca AA095616 AA093614 AA095550 AA095620
ABTC11932_aca
ABTC72881_aca
ABTC8929_aca
ABTC8938_aca
AA095616 0.14080744
AA093614 0.13065543 0.08678606
AA095550 0.12737336 0.08626468 0.06292768
AA095620 0.08508519 0.14121521 0.12965296 0.12677222
AA095553 0.32049149 0.32998325 0.31788160 0.31575779 0.31824280
AA095548 0.31601644 0.32376396 0.31340504 0.31138502 0.31375667
AA095617 0.14068990 0.04621888 0.08742573 0.08650916 0.14140623
AA093615 0.12977855 0.08841884 0.06305928 0.06167350 0.12855024
AA095626 0.12955431 0.08667520 0.06343646 0.06060468 0.12962919
AA095636 0.08637781 0.14572803 0.13587765 0.13223899 0.08789149
AA095546 0.31362790 0.32429397 0.31249170 0.31110395 0.31095495
AA096028 0.14251904 0.05059806 0.08862362 0.08521521 0.14207077
AA095562 0.12937856 0.08782714 0.05961851 0.06241020 0.12924603
AA095623 0.12932203 0.08756431 0.06422775 0.06061574 0.12932390
AA095635 0.08542981 0.14254812 0.13117772 0.12801478 0.08521251
AA095547 0.31254715 0.32151812 0.30977227 0.30868648 0.31000947
AA096030 0.14189850 0.05053547 0.08806557 0.08551761 0.14125691
AA095629 0.12882123 0.08619119 0.06437394 0.05970354 0.12853692
AA095624 0.12833686 0.08627574 0.06229852 0.05984714 0.12816978
AA095637 0.08614294 0.14745168 0.13509229 0.13170790 0.08641127
AA095545 0.31602387 0.32495526 0.31336418 0.31270592 0.31432967
AA095568 0.12759969 0.08611324 0.06378782 0.06009052 0.12735961
AA095625 0.12938245 0.08696716 0.06325949 0.05972007 0.12873366
AA095542 0.31661065 0.32540439 0.31401151 0.31246329 0.31431394
AA095570 0.14327493 0.05170547 0.08973352 0.08717393 0.14286584
AA095549 0.12892716 0.08774660 0.06116545 0.06216928 0.12857554
AA095551 0.14228480 0.05154941 0.09015148 0.08739275 0.14229508
AA095543 0.31918316 0.32754955 0.31557041 0.31386374 0.31621192
AA096029 0.14301233 0.05329794 0.09180275 0.08879880 0.14311669
AA095627 0.14095951 0.05025390 0.08603755 0.08504056 0.14005179
AA095540 0.12939861 0.08779664 0.06551237 0.06225029 0.12987653
AA095544 0.31579404 0.32453682 0.31230384 0.31102992 0.31394411
AA095634 0.14254177 0.05200826 0.09017185 0.08735654 0.14213807
AA095569 0.12921947 0.08781870 0.06429757 0.06114564 0.12912740
AA095539a 0.31581439 0.32352226 0.31305452 0.31195574 0.31291427
AA095553 AA095548 AA095617 AA093615 AA095626 AA095636
ABTC11932_aca
ABTC72881_aca
ABTC8929_aca
ABTC8938_aca
AA095616
AA093614
AA095550
AA095620
AA095553
AA095548 0.13256956
AA095617 0.33089508 0.32464320
AA093615 0.31724608 0.31193351 0.08839889
AA095626 0.31527201 0.31075000 0.08694741 0.03364938
AA095636 0.32506875 0.31822304 0.14628306 0.13415417 0.13457442
AA095546 0.13643491 0.13229662 0.32558840 0.31157869 0.30984602 0.31666481
AA096028 0.32914573 0.32416224 0.04992833 0.08827145 0.08693631 0.14716467
AA095562 0.31608899 0.31171344 0.08830582 0.06097394 0.06085567 0.13443139
AA095623 0.31637475 0.31208733 0.08823392 0.03539683 0.02798696 0.13472416
AA095635 0.32174888 0.31548405 0.14306562 0.12967495 0.12932462 0.08565490
AA095547 0.13787410 0.13184008 0.32255030 0.31029298 0.30892445 0.31549152
AA096030 0.32942168 0.32292085 0.05045667 0.08874684 0.08738178 0.14642960
AA095629 0.31512170 0.31085470 0.08667726 0.05506653 0.03393092 0.13368724
AA095624 0.31654082 0.31211803 0.08679105 0.03530623 0.03363794 0.13384089
AA095637 0.32080777 0.31806665 0.14716351 0.13395858 0.13460763 0.08786402
AA095545 0.13651325 0.13323251 0.32681564 0.31353957 0.31223785 0.31887713
AA095568 0.31649923 0.31119569 0.08663958 0.05769056 0.05673038 0.13268005
AA095625 0.31612087 0.31132771 0.08703557 0.03487633 0.02959312 0.13447549
AA095542 0.13577795 0.13287985 0.32634633 0.31327768 0.31228976 0.31829619
AA095570 0.32902223 0.32287158 0.05127300 0.08920974 0.08714534 0.14842900
AA095549 0.31587783 0.31065472 0.08760149 0.06302146 0.06219534 0.13417333
AA095551 0.32990947 0.32503217 0.05106563 0.09047166 0.08976934 0.14725102
AA095543 0.13425109 0.12989502 0.32823199 0.31459298 0.31365191 0.32087072
AA096029 0.33015877 0.32378540 0.05391313 0.09131175 0.08974954 0.14816340
AA095627 0.32834276 0.32255565 0.04947125 0.08750058 0.08565806 0.14576422
AA095540 0.31593782 0.31145889 0.08761641 0.06193108 0.06149244 0.13461171
AA095544 0.13366468 0.13062818 0.32531973 0.31199330 0.31119519 0.31770948
AA095634 0.32956274 0.32407482 0.05115303 0.08920753 0.08764361 0.14659825
AA095569 0.31697344 0.31241060 0.08835102 0.06159852 0.06075713 0.13437068
AA095539a 0.13431550 0.13100307 0.32520523 0.31298616 0.31202731 0.31858067
AA095546 AA096028 AA095562 AA095623 AA095635 AA095547
ABTC11932_aca
ABTC72881_aca
ABTC8929_aca
ABTC8938_aca
AA095616
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028 0.32455743
AA095562 0.31221677 0.08794511
AA095623 0.31131322 0.08768589 0.06094550
AA095635 0.31559237 0.14293665 0.13059436 0.12974316
AA095547 0.12539362 0.32230058 0.30966075 0.31016163 0.31229070
AA096030 0.32430196 0.04735877 0.08836485 0.08805626 0.14282961 0.32162986
AA095629 0.31084479 0.08632537 0.06115443 0.03355674 0.12888741 0.30909260
AA095624 0.31132376 0.08571299 0.06056771 0.02962980 0.12919027 0.30952003
AA095637 0.31642781 0.14721800 0.13503086 0.13427310 0.08341461 0.31333001
AA095545 0.13144768 0.32619475 0.31298818 0.31334090 0.31617039 0.13084569
AA095568 0.31064090 0.08705635 0.06192790 0.05737427 0.12791055 0.30863806
AA095625 0.31109569 0.08699698 0.06102429 0.02986604 0.12892985 0.30944548
AA095542 0.13114873 0.32483646 0.31323019 0.31356067 0.31613885 0.13276991
AA095570 0.32395479 0.03821203 0.08823189 0.08878645 0.14385914 0.32119241
AA095549 0.31028711 0.08847863 0.06390318 0.06296549 0.12945600 0.30884350
AA095551 0.32557097 0.04906167 0.08891378 0.09039065 0.14326554 0.32177308
AA095543 0.13007471 0.32706687 0.31516148 0.31501365 0.31947099 0.13114116
AA096029 0.32422984 0.04767337 0.09102516 0.09082262 0.14430205 0.32133449
AA095627 0.32341082 0.04464449 0.08719926 0.08698304 0.14114280 0.32044824
AA095540 0.31200280 0.08709663 0.06370568 0.06143676 0.13069307 0.30879758
AA095544 0.13178003 0.32475974 0.31232949 0.31233624 0.31651224 0.13071585
AA095634 0.32484949 0.04598886 0.08874634 0.08904473 0.14308616 0.32237819
AA095569 0.31258888 0.08840510 0.06335043 0.06078681 0.12983439 0.30915980
AA095539a 0.13152827 0.32472480 0.31243759 0.31309883 0.31780010 0.12930911
AA096030 AA095629 AA095624 AA095637 AA095545 AA095568
ABTC11932_aca
ABTC72881_aca
ABTC8929_aca
ABTC8938_aca
AA095616
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028
AA095562
AA095623
AA095635
AA095547
AA096030
AA095629 0.08696658
AA095624 0.08626202 0.03330168
AA095637 0.14685931 0.13334048 0.13359050
AA095545 0.32514975 0.31263063 0.31367701 0.31855084
AA095568 0.08733609 0.05725295 0.05578466 0.13267915 0.31208080
AA095625 0.08687419 0.03357051 0.02841547 0.13435548 0.31244552 0.05396822
AA095542 0.32334546 0.31266621 0.31335517 0.31890594 0.13078863 0.31226555
AA095570 0.04853950 0.08681556 0.08627419 0.14777161 0.32504723 0.08869328
AA095549 0.08738697 0.06172205 0.06112322 0.13324189 0.31205608 0.06039514
AA095551 0.04918395 0.08889146 0.08839442 0.14807163 0.32583802 0.08890859
AA095543 0.32652951 0.31408346 0.31404784 0.31944097 0.12723080 0.31335272
AA096029 0.05121461 0.08876394 0.08902335 0.14922636 0.32657999 0.09038502
AA095627 0.04773444 0.08604834 0.08472028 0.14601258 0.32471395 0.08624569
AA095540 0.08826607 0.06161968 0.06096895 0.13499545 0.31264790 0.06200474
AA095544 0.32449216 0.31129795 0.31193242 0.31684114 0.12879307 0.31012859
AA095634 0.04878956 0.08773148 0.08725959 0.14808463 0.32628736 0.08800230
AA095569 0.08756439 0.06062960 0.06035364 0.13409335 0.31376765 0.06288358
AA095539a 0.32405304 0.31162055 0.31274707 0.31735737 0.13268788 0.31195003
AA095625 AA095542 AA095570 AA095549 AA095551 AA095543
ABTC11932_aca
ABTC72881_aca
ABTC8929_aca
ABTC8938_aca
AA095616
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028
AA095562
AA095623
AA095635
AA095547
AA096030
AA095629
AA095624
AA095637
AA095545
AA095568
AA095625
AA095542 0.31266575
AA095570 0.08740318 0.32539532
AA095549 0.06197565 0.31191635 0.08966095
AA095551 0.08911189 0.32564075 0.04956806 0.09000905
AA095543 0.31400658 0.12441947 0.32805086 0.31362910 0.32733366
AA096029 0.08937366 0.32582974 0.04907738 0.09083063 0.04942303 0.32839328
AA095627 0.08559181 0.32409451 0.04110066 0.08718791 0.04936365 0.32652236
AA095540 0.06140551 0.31208592 0.08758136 0.06438560 0.08926535 0.31476137
AA095544 0.31165319 0.12388355 0.32464949 0.31040625 0.32560650 0.12329120
AA095634 0.08772173 0.32616434 0.04782081 0.08963205 0.05024179 0.32772451
AA095569 0.05967139 0.31391008 0.08853196 0.06395083 0.08950890 0.31518086
AA095539a 0.31255259 0.13192559 0.32418748 0.31151328 0.32534540 0.13071839
AA096029 AA095627 AA095540 AA095544 AA095634 AA095569
ABTC11932_aca
ABTC72881_aca
ABTC8929_aca
ABTC8938_aca
AA095616
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028
AA095562
AA095623
AA095635
AA095547
AA096030
AA095629
AA095624
AA095637
AA095545
AA095568
AA095625
AA095542
AA095570
AA095549
AA095551
AA095543
AA096029
AA095627 0.04966153
AA095540 0.08978857 0.08732479
AA095544 0.32497694 0.32375252 0.31138196
AA095634 0.05006785 0.04752622 0.08864646 0.32527701
AA095569 0.08998039 0.08654804 0.06300766 0.31173884 0.08800186
AA095539a 0.32503093 0.32269768 0.31156178 0.13118967 0.32574257 0.31221582
$Dgeo
ABTC11930_aca ABTC11932_aca ABTC72881_aca ABTC8929_aca
ABTC11932_aca 1.479506e-01
ABTC72881_aca 2.559400e+05 2.559401e+05
ABTC8929_aca 2.647148e+05 2.647146e+05 3.105123e+05
ABTC8938_aca 1.806023e+05 1.806022e+05 1.979688e+05 1.206174e+05
AA095616 7.732494e+05 7.732492e+05 1.008649e+06 7.735525e+05
AA093614 4.289002e+05 4.289002e+05 6.680925e+05 6.395803e+05
AA095550 4.315584e+05 4.315584e+05 6.759576e+05 6.314426e+05
AA095620 1.745281e+05 1.745280e+05 1.842651e+05 1.353572e+05
AA095553 4.648706e+05 4.648707e+05 5.853559e+05 7.294889e+05
AA095548 4.647510e+05 4.647511e+05 5.844383e+05 7.293445e+05
AA095617 7.466274e+05 7.466273e+05 9.820426e+05 7.480617e+05
AA093615 4.288560e+05 4.288560e+05 6.680680e+05 6.395041e+05
AA095626 4.288551e+05 4.288551e+05 6.680683e+05 6.395011e+05
AA095636 1.815843e+05 1.815842e+05 2.155105e+05 1.059797e+05
AA095546 4.648706e+05 4.648708e+05 5.853559e+05 7.294890e+05
AA096028 6.002876e+05 6.002875e+05 8.345819e+05 6.060720e+05
AA095562 4.288563e+05 4.288563e+05 6.680679e+05 6.395051e+05
AA095623 4.288549e+05 4.288549e+05 6.680683e+05 6.395004e+05
AA095635 1.815874e+05 1.815873e+05 2.155151e+05 1.059746e+05
AA095547 4.648673e+05 4.648675e+05 5.853538e+05 7.294857e+05
AA096030 6.002854e+05 6.002853e+05 8.345800e+05 6.060709e+05
AA095629 4.288561e+05 4.288561e+05 6.680680e+05 6.395043e+05
AA095624 4.288558e+05 4.288558e+05 6.680681e+05 6.395033e+05
AA095637 1.745293e+05 1.745293e+05 1.842675e+05 1.353545e+05
AA095545 4.917123e+05 4.917124e+05 5.912690e+05 7.550987e+05
AA095568 4.447169e+05 4.447169e+05 6.839464e+05 6.542060e+05
AA095625 4.288562e+05 4.288563e+05 6.680679e+05 6.395049e+05
AA095542 4.759495e+05 4.759496e+05 5.794111e+05 7.395803e+05
AA095570 6.002926e+05 6.002925e+05 8.345862e+05 6.060745e+05
AA095549 4.447172e+05 4.447172e+05 6.839463e+05 6.542070e+05
AA095551 6.009385e+05 6.009384e+05 8.349173e+05 6.057533e+05
AA095543 4.759425e+05 4.759426e+05 5.793617e+05 7.395693e+05
AA096029 6.003361e+05 6.003360e+05 8.346206e+05 6.060886e+05
AA095627 6.002880e+05 6.002879e+05 8.345822e+05 6.060722e+05
AA095540 4.409964e+05 4.409964e+05 6.824284e+05 6.465696e+05
AA095544 4.757600e+05 4.757601e+05 5.792618e+05 7.393929e+05
AA095634 6.003280e+05 6.003279e+05 8.346130e+05 6.060825e+05
AA095569 4.324983e+05 4.324983e+05 6.766541e+05 6.328738e+05
AA095539a 4.647550e+05 4.647551e+05 5.852496e+05 7.293733e+05
ABTC8938_aca AA095616 AA093614 AA095550 AA095620
ABTC11932_aca
ABTC72881_aca
ABTC8929_aca
ABTC8938_aca
AA095616 8.327245e+05
AA093614 5.982879e+05 6.174851e+05
AA095550 5.963781e+05 5.835782e+05 3.391609e+04
AA095620 1.479670e+04 8.419934e+05 5.960629e+05 5.949874e+05
AA095553 6.334209e+05 9.798642e+05 3.712245e+05 4.037582e+05 6.231797e+05
AA095548 6.330729e+05 9.812641e+05 3.728293e+05 4.053365e+05 6.227998e+05
AA095617 8.064215e+05 2.665915e+04 5.962914e+05 5.623756e+05 8.156321e+05
AA093615 5.982301e+05 6.173752e+05 1.211815e+02 3.380511e+04 5.960078e+05
AA095626 5.982283e+05 6.173684e+05 1.279293e+02 3.379828e+04 5.960062e+05
AA095636 1.759474e+04 8.168964e+05 5.934916e+05 5.906269e+05 3.156877e+04
AA095546 6.334210e+05 9.798643e+05 3.712245e+05 4.037583e+05 6.231798e+05
AA096028 6.600335e+05 1.740869e+05 4.953333e+05 4.621578e+05 6.689795e+05
AA095562 5.982307e+05 6.173776e+05 1.188520e+02 3.380748e+04 5.960083e+05
AA095623 5.982279e+05 6.173668e+05 1.294963e+02 3.379670e+04 5.960058e+05
AA095635 1.759910e+04 8.168936e+05 5.934930e+05 5.906280e+05 3.157358e+04
AA095547 6.334180e+05 9.798605e+05 3.712210e+05 4.037547e+05 6.231768e+05
AA096030 6.600319e+05 1.740889e+05 4.953303e+05 4.621548e+05 6.689779e+05
AA095629 5.982302e+05 6.173757e+05 1.206880e+02 3.380561e+04 5.960079e+05
AA095624 5.982296e+05 6.173735e+05 1.228971e+02 3.380337e+04 5.960074e+05
AA095637 1.479403e+04 8.419919e+05 5.960636e+05 5.949879e+05 2.682530e+00
AA095545 6.544681e+05 1.029991e+06 4.221159e+05 4.546300e+05 6.434768e+05
AA095568 6.137958e+05 6.151320e+05 1.589271e+04 3.540922e+04 6.116504e+05
AA095625 5.982305e+05 6.173771e+05 1.193680e+02 3.380695e+04 5.960082e+05
AA095542 6.396142e+05 1.015144e+06 4.088057e+05 4.410892e+05 6.287432e+05
AA095570 6.600370e+05 1.740826e+05 4.953402e+05 4.621647e+05 6.689832e+05
AA095549 6.137964e+05 6.151343e+05 1.589278e+04 3.541152e+04 6.116509e+05
AA095551 6.600919e+05 1.737321e+05 4.972879e+05 4.641276e+05 6.690772e+05
AA095543 6.395936e+05 1.015212e+06 4.088855e+05 4.411675e+05 6.287210e+05
AA096029 6.600631e+05 1.740471e+05 4.954125e+05 4.622372e+05 6.690104e+05
AA095627 6.600337e+05 1.740866e+05 4.953339e+05 4.621584e+05 6.689798e+05
AA095540 6.084028e+05 6.018546e+05 1.913132e+04 2.159549e+04 6.065700e+05
AA095544 6.394333e+05 1.014979e+06 4.086623e+05 4.409426e+05 6.285635e+05
AA095634 6.600561e+05 1.740548e+05 4.954047e+05 4.622294e+05 6.690034e+05
AA095569 5.975481e+05 5.850930e+05 3.239465e+04 1.908246e+03 5.961199e+05
AA095539a 6.333057e+05 9.797935e+05 3.711706e+05 4.037018e+05 6.230647e+05
AA095553 AA095548 AA095617 AA093615 AA095626
ABTC11932_aca
ABTC72881_aca
ABTC8929_aca
ABTC8938_aca
AA095616
AA093614
AA095550
AA095620
AA095553
AA095548 1.916028e+03
AA095617 9.570266e+05 9.584078e+05
AA093615 3.713162e+05 3.729208e+05 5.961802e+05
AA095626 3.713224e+05 3.729270e+05 5.961734e+05 6.937866e+00
AA095636 6.391648e+05 6.388662e+05 7.906359e+05 5.934308e+05 5.934289e+05
AA095546 6.285262e-02 1.915997e+03 9.570267e+05 3.713163e+05 3.713225e+05
AA096028 8.400489e+05 8.412906e+05 1.474645e+05 4.952148e+05 4.952079e+05
AA095562 3.713141e+05 3.729187e+05 5.961826e+05 2.400323e+00 9.338189e+00
AA095623 3.713238e+05 3.729284e+05 5.961718e+05 8.546075e+00 1.608209e+00
AA095635 6.391688e+05 6.388701e+05 7.906332e+05 5.934322e+05 5.934303e+05
AA095547 3.875288e+00 1.917960e+03 9.570229e+05 3.713128e+05 3.713190e+05
AA096030 8.400460e+05 8.412876e+05 1.474664e+05 4.952118e+05 4.952049e+05
AA095629 3.713158e+05 3.729204e+05 5.961807e+05 5.082852e-01 7.446151e+00
AA095624 3.713178e+05 3.729224e+05 5.961785e+05 1.765922e+00 5.171943e+00
AA095637 6.231817e+05 6.228018e+05 8.156306e+05 5.960084e+05 5.960068e+05
AA095545 5.089205e+04 4.929430e+04 1.007028e+06 4.222076e+05 4.222138e+05
AA095568 3.782367e+05 3.798801e+05 5.943659e+05 1.592592e+04 1.592619e+04
AA095625 3.713146e+05 3.729191e+05 5.961821e+05 1.868420e+00 8.806286e+00
AA095542 3.881126e+04 3.699378e+04 9.920808e+05 4.088955e+05 4.089016e+05
AA095570 8.400557e+05 8.412973e+05 1.474601e+05 4.952217e+05 4.952148e+05
AA095549 3.782347e+05 3.798780e+05 5.943683e+05 1.592601e+04 1.592629e+04
AA095551 8.417367e+05 8.429759e+05 1.471312e+05 4.971693e+05 4.971624e+05
AA095543 3.890289e+04 3.708478e+04 9.921476e+05 4.089752e+05 4.089813e+05
AA096029 8.401240e+05 8.413656e+05 1.474252e+05 4.952940e+05 4.952871e+05
AA095627 8.400495e+05 8.412911e+05 1.474641e+05 4.952154e+05 4.952084e+05
AA095540 3.893781e+05 3.909992e+05 5.809683e+05 1.907035e+04 1.906554e+04
AA095544 3.870400e+04 3.688393e+04 9.919143e+05 4.087520e+05 4.087582e+05
AA095634 8.401155e+05 8.413571e+05 1.474328e+05 4.952861e+05 4.952792e+05
AA095569 4.025826e+05 4.041650e+05 5.639225e+05 3.228544e+04 3.227865e+04
AA095539a 1.156729e+02 1.908561e+03 9.569547e+05 3.712623e+05 3.712685e+05
AA095636 AA095546 AA096028 AA095562 AA095623
ABTC11932_aca
ABTC72881_aca
ABTC8929_aca
ABTC8938_aca
AA095616
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546 6.391649e+05
AA096028 6.444533e+05 8.400490e+05
AA095562 5.934315e+05 3.713141e+05 4.952172e+05
AA095623 5.934284e+05 3.713239e+05 4.952063e+05 1.094640e+01
AA095635 5.104533e+00 6.391688e+05 6.444507e+05 5.934329e+05 5.934298e+05
AA095547 6.391618e+05 3.938140e+00 8.400451e+05 3.713106e+05 3.713204e+05
AA096030 6.444518e+05 8.400460e+05 3.014050e+00 4.952142e+05 4.952033e+05
AA095629 5.934309e+05 3.713158e+05 4.952153e+05 1.892038e+00 9.054360e+00
AA095624 5.934303e+05 3.713179e+05 4.952131e+05 4.166246e+00 6.780152e+00
AA095637 3.156624e+04 6.231818e+05 6.689781e+05 5.960089e+05 5.960064e+05
AA095545 6.613808e+05 5.089200e+04 8.889012e+05 4.222055e+05 4.222152e+05
AA095568 6.088960e+05 3.782368e+05 4.965936e+05 1.592582e+04 1.592626e+04
AA095625 5.934313e+05 3.713146e+05 4.952167e+05 5.319035e-01 1.041449e+01
AA095542 6.463415e+05 3.881121e+04 8.733243e+05 4.088934e+05 4.089030e+05
AA095570 6.444568e+05 8.400557e+05 6.861102e+00 4.952241e+05 4.952132e+05
AA095549 6.088967e+05 3.782347e+05 4.965960e+05 1.592592e+04 1.592636e+04
AA095551 6.444840e+05 8.417368e+05 2.216430e+03 4.971717e+05 4.971608e+05
AA095543 6.463233e+05 3.890284e+04 8.733838e+05 4.089731e+05 4.089828e+05
AA096029 6.444820e+05 8.401240e+05 7.992089e+01 4.952964e+05 4.952855e+05
AA095627 6.444536e+05 8.400495e+05 5.364397e-01 4.952178e+05 4.952068e+05
AA095540 6.031469e+05 3.893782e+05 4.826337e+05 1.907201e+04 1.906443e+04
AA095544 6.461587e+05 3.870395e+04 8.731489e+05 4.087499e+05 4.087596e+05
AA095634 6.444750e+05 8.401156e+05 7.277465e+01 4.952885e+05 4.952776e+05
AA095569 5.918387e+05 4.025827e+05 4.639055e+05 3.228779e+04 3.227708e+04
AA095539a 6.390494e+05 1.157242e+02 8.399682e+05 3.712602e+05 3.712699e+05
AA095635 AA095547 AA096030 AA095629 AA095624
ABTC11932_aca
ABTC72881_aca
ABTC8929_aca
ABTC8938_aca
AA095616
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028
AA095562
AA095623
AA095635
AA095547 6.391658e+05
AA096030 6.444491e+05 8.400422e+05
AA095629 5.934324e+05 3.713123e+05 4.952123e+05
AA095624 5.934317e+05 3.713143e+05 4.952101e+05 2.274208e+00
AA095637 3.157105e+04 6.231788e+05 6.689765e+05 5.960085e+05 5.960080e+05
AA095545 6.613850e+05 5.089550e+04 8.888983e+05 4.222072e+05 4.222092e+05
AA095568 6.088974e+05 3.782334e+05 4.965906e+05 1.592589e+04 1.592599e+04
AA095625 5.934328e+05 3.713111e+05 4.952137e+05 1.360135e+00 3.634342e+00
AA095542 6.463456e+05 3.881413e+04 8.733213e+05 4.088950e+05 4.088970e+05
AA095570 6.444542e+05 8.400519e+05 9.875152e+00 4.952222e+05 4.952199e+05
AA095549 6.088981e+05 3.782313e+05 4.965930e+05 1.592599e+04 1.592608e+04
AA095551 6.444814e+05 8.417329e+05 2.219042e+03 4.971699e+05 4.971676e+05
AA095543 6.463274e+05 3.890576e+04 8.733809e+05 4.089748e+05 4.089768e+05
AA096029 6.444794e+05 8.401202e+05 8.289407e+01 4.952945e+05 4.952922e+05
AA095627 6.444510e+05 8.400456e+05 3.550489e+00 4.952159e+05 4.952136e+05
AA095540 6.031482e+05 3.893747e+05 4.826307e+05 1.907070e+04 1.906913e+04
AA095544 6.461629e+05 3.870686e+04 8.731459e+05 4.087516e+05 4.087536e+05
AA095634 6.444724e+05 8.401117e+05 7.571145e+01 4.952867e+05 4.952844e+05
AA095569 5.918399e+05 4.025791e+05 4.639025e+05 3.228594e+04 3.228371e+04
AA095539a 6.390533e+05 1.125312e+02 8.399653e+05 3.712619e+05 3.712639e+05
AA095637 AA095545 AA095568 AA095625 AA095542
ABTC11932_aca
ABTC72881_aca
ABTC8929_aca
ABTC8938_aca
AA095616
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028
AA095562
AA095623
AA095635
AA095547
AA096030
AA095629
AA095624
AA095637
AA095545 6.434790e+05
AA095568 6.116510e+05 4.291045e+05
AA095625 5.960088e+05 4.222060e+05 1.592584e+04
AA095542 6.287453e+05 1.669474e+04 4.161431e+05 4.088938e+05
AA095570 6.689818e+05 8.889080e+05 4.966005e+05 4.952236e+05 8.733310e+05
AA095549 6.116516e+05 4.291024e+05 2.401226e+00 1.592594e+04 4.161411e+05
AA095551 6.690757e+05 8.905650e+05 4.985805e+05 4.971712e+05 8.749781e+05
AA095543 6.287231e+05 1.666843e+04 4.162249e+05 4.089736e+05 9.944637e+01
AA096029 6.690090e+05 8.889758e+05 4.966731e+05 4.952959e+05 8.733987e+05
AA095627 6.689784e+05 8.889018e+05 4.965942e+05 4.952172e+05 8.733248e+05
AA095540 6.065705e+05 4.402676e+05 1.402144e+04 1.907165e+04 4.270970e+05
AA095544 6.285656e+05 1.688971e+04 4.160044e+05 4.087504e+05 1.957239e+02
AA095634 6.690019e+05 8.889673e+05 4.966654e+05 4.952880e+05 8.733902e+05
AA095569 5.961204e+05 4.534591e+05 3.353010e+04 3.228727e+04 4.399516e+05
AA095539a 6.230667e+05 5.094551e+04 3.781868e+05 3.712607e+05 3.883660e+04
AA095570 AA095549 AA095551 AA095543 AA096029
ABTC11932_aca
ABTC72881_aca
ABTC8929_aca
ABTC8938_aca
AA095616
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028
AA095562
AA095623
AA095635
AA095547
AA096030
AA095629
AA095624
AA095637
AA095545
AA095568
AA095625
AA095542
AA095570
AA095549 4.966029e+05
AA095551 2.210488e+03 4.985829e+05
AA095543 8.733906e+05 4.162228e+05 8.750375e+05
AA096029 7.316530e+01 4.966755e+05 2.141666e+03 8.734582e+05
AA095627 6.324663e+00 4.965966e+05 2.215965e+03 8.733844e+05 7.939205e+01
AA095540 4.826406e+05 1.402381e+04 4.846180e+05 4.271775e+05 4.827132e+05
AA095544 8.731556e+05 4.160023e+05 8.748025e+05 2.350750e+02 8.732232e+05
AA095634 6.611534e+01 4.966678e+05 2.146821e+03 8.734497e+05 8.635395e+00
AA095569 4.639124e+05 3.353241e+04 4.658770e+05 4.400301e+05 4.639849e+05
AA095539a 8.399750e+05 3.781847e+05 8.416559e+05 3.892812e+04 8.400433e+05
AA095627 AA095540 AA095544 AA095634 AA095569
ABTC11932_aca
ABTC72881_aca
ABTC8929_aca
ABTC8938_aca
AA095616
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028
AA095562
AA095623
AA095635
AA095547
AA096030
AA095629
AA095624
AA095637
AA095545
AA095568
AA095625
AA095542
AA095570
AA095549
AA095551
AA095543
AA096029
AA095627
AA095540 4.826343e+05
AA095544 8.731494e+05 4.269554e+05
AA095634 7.225263e+01 4.827054e+05 8.732148e+05
AA095569 4.639061e+05 1.969448e+04 4.398054e+05 4.639771e+05
AA095539a 8.399688e+05 3.893259e+05 3.872887e+04 8.400348e+05 4.025266e+05
$mantel
Mantel statistic based on Pearson's product-moment correlation
Call:
vegan::mantel(xdis = Dgen, ydis = Dgeo, permutations = permutations, na.rm = TRUE)
Mantel statistic r: 0.5168
Significance: 0.001
Upper quantiles of permutations (null model):
90% 95% 97.5% 99%
0.0795 0.1093 0.1340 0.1654
Permutation: free
Number of permutations: 999# karyo
gl.ibd(vac.gl18, distance = "propShared",
paircols = "pop", Dgeo_trans = "Dgeo")Starting gl.ibd
Analysis performed on the genlight object.
Coordinates transformed to Mercator (google) projection to calculate distances in meters.
Coordinates used from: x@other$latlon (Mercator transformed)
Transformation of Dgeo: Dgeo
Genetic distance: propShared
Tranformation of Dgen: Dgen
Mantel statistic based on Pearson's product-moment correlation
Call:
vegan::mantel(xdis = Dgen, ydis = Dgeo, permutations = permutations, na.rm = TRUE)
Mantel statistic r: 0.5604
Significance: 0.001
Upper quantiles of permutations (null model):
90% 95% 97.5% 99%
0.090 0.119 0.154 0.183
Permutation: free
Number of permutations: 999
Completed: gl.ibd $Dgen
AA095616 AA093614 AA095550 AA095620 AA095553 AA095548
AA093614 0.08678606
AA095550 0.08626468 0.06292768
AA095620 0.14121521 0.12965296 0.12677222
AA095553 0.32998325 0.31788160 0.31575779 0.31824280
AA095548 0.32376396 0.31340504 0.31138502 0.31375667 0.13256956
AA095617 0.04621888 0.08742573 0.08650916 0.14140623 0.33089508 0.32464320
AA093615 0.08841884 0.06305928 0.06167350 0.12855024 0.31724608 0.31193351
AA095626 0.08667520 0.06343646 0.06060468 0.12962919 0.31527201 0.31075000
AA095636 0.14572803 0.13587765 0.13223899 0.08789149 0.32506875 0.31822304
AA095546 0.32429397 0.31249170 0.31110395 0.31095495 0.13643491 0.13229662
AA096028 0.05059806 0.08862362 0.08521521 0.14207077 0.32914573 0.32416224
AA095562 0.08782714 0.05961851 0.06241020 0.12924603 0.31608899 0.31171344
AA095623 0.08756431 0.06422775 0.06061574 0.12932390 0.31637475 0.31208733
AA095635 0.14254812 0.13117772 0.12801478 0.08521251 0.32174888 0.31548405
AA095547 0.32151812 0.30977227 0.30868648 0.31000947 0.13787410 0.13184008
AA096030 0.05053547 0.08806557 0.08551761 0.14125691 0.32942168 0.32292085
AA095629 0.08619119 0.06437394 0.05970354 0.12853692 0.31512170 0.31085470
AA095624 0.08627574 0.06229852 0.05984714 0.12816978 0.31654082 0.31211803
AA095637 0.14745168 0.13509229 0.13170790 0.08641127 0.32080777 0.31806665
AA095545 0.32495526 0.31336418 0.31270592 0.31432967 0.13651325 0.13323251
AA095568 0.08611324 0.06378782 0.06009052 0.12735961 0.31649923 0.31119569
AA095625 0.08696716 0.06325949 0.05972007 0.12873366 0.31612087 0.31132771
AA095542 0.32540439 0.31401151 0.31246329 0.31431394 0.13577795 0.13287985
AA095570 0.05170547 0.08973352 0.08717393 0.14286584 0.32902223 0.32287158
AA095543 0.32754955 0.31557041 0.31386374 0.31621192 0.13425109 0.12989502
AA096029 0.05329794 0.09180275 0.08879880 0.14311669 0.33015877 0.32378540
AA095627 0.05025390 0.08603755 0.08504056 0.14005179 0.32834276 0.32255565
AA095544 0.32453682 0.31230384 0.31102992 0.31394411 0.13366468 0.13062818
AA095634 0.05200826 0.09017185 0.08735654 0.14213807 0.32956274 0.32407482
AA095569 0.08781870 0.06429757 0.06114564 0.12912740 0.31697344 0.31241060
AA095617 AA093615 AA095626 AA095636 AA095546 AA096028
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615 0.08839889
AA095626 0.08694741 0.03364938
AA095636 0.14628306 0.13415417 0.13457442
AA095546 0.32558840 0.31157869 0.30984602 0.31666481
AA096028 0.04992833 0.08827145 0.08693631 0.14716467 0.32455743
AA095562 0.08830582 0.06097394 0.06085567 0.13443139 0.31221677 0.08794511
AA095623 0.08823392 0.03539683 0.02798696 0.13472416 0.31131322 0.08768589
AA095635 0.14306562 0.12967495 0.12932462 0.08565490 0.31559237 0.14293665
AA095547 0.32255030 0.31029298 0.30892445 0.31549152 0.12539362 0.32230058
AA096030 0.05045667 0.08874684 0.08738178 0.14642960 0.32430196 0.04735877
AA095629 0.08667726 0.05506653 0.03393092 0.13368724 0.31084479 0.08632537
AA095624 0.08679105 0.03530623 0.03363794 0.13384089 0.31132376 0.08571299
AA095637 0.14716351 0.13395858 0.13460763 0.08786402 0.31642781 0.14721800
AA095545 0.32681564 0.31353957 0.31223785 0.31887713 0.13144768 0.32619475
AA095568 0.08663958 0.05769056 0.05673038 0.13268005 0.31064090 0.08705635
AA095625 0.08703557 0.03487633 0.02959312 0.13447549 0.31109569 0.08699698
AA095542 0.32634633 0.31327768 0.31228976 0.31829619 0.13114873 0.32483646
AA095570 0.05127300 0.08920974 0.08714534 0.14842900 0.32395479 0.03821203
AA095543 0.32823199 0.31459298 0.31365191 0.32087072 0.13007471 0.32706687
AA096029 0.05391313 0.09131175 0.08974954 0.14816340 0.32422984 0.04767337
AA095627 0.04947125 0.08750058 0.08565806 0.14576422 0.32341082 0.04464449
AA095544 0.32531973 0.31199330 0.31119519 0.31770948 0.13178003 0.32475974
AA095634 0.05115303 0.08920753 0.08764361 0.14659825 0.32484949 0.04598886
AA095569 0.08835102 0.06159852 0.06075713 0.13437068 0.31258888 0.08840510
AA095562 AA095623 AA095635 AA095547 AA096030 AA095629
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028
AA095562
AA095623 0.06094550
AA095635 0.13059436 0.12974316
AA095547 0.30966075 0.31016163 0.31229070
AA096030 0.08836485 0.08805626 0.14282961 0.32162986
AA095629 0.06115443 0.03355674 0.12888741 0.30909260 0.08696658
AA095624 0.06056771 0.02962980 0.12919027 0.30952003 0.08626202 0.03330168
AA095637 0.13503086 0.13427310 0.08341461 0.31333001 0.14685931 0.13334048
AA095545 0.31298818 0.31334090 0.31617039 0.13084569 0.32514975 0.31263063
AA095568 0.06192790 0.05737427 0.12791055 0.30863806 0.08733609 0.05725295
AA095625 0.06102429 0.02986604 0.12892985 0.30944548 0.08687419 0.03357051
AA095542 0.31323019 0.31356067 0.31613885 0.13276991 0.32334546 0.31266621
AA095570 0.08823189 0.08878645 0.14385914 0.32119241 0.04853950 0.08681556
AA095543 0.31516148 0.31501365 0.31947099 0.13114116 0.32652951 0.31408346
AA096029 0.09102516 0.09082262 0.14430205 0.32133449 0.05121461 0.08876394
AA095627 0.08719926 0.08698304 0.14114280 0.32044824 0.04773444 0.08604834
AA095544 0.31232949 0.31233624 0.31651224 0.13071585 0.32449216 0.31129795
AA095634 0.08874634 0.08904473 0.14308616 0.32237819 0.04878956 0.08773148
AA095569 0.06335043 0.06078681 0.12983439 0.30915980 0.08756439 0.06062960
AA095624 AA095637 AA095545 AA095568 AA095625 AA095542
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028
AA095562
AA095623
AA095635
AA095547
AA096030
AA095629
AA095624
AA095637 0.13359050
AA095545 0.31367701 0.31855084
AA095568 0.05578466 0.13267915 0.31208080
AA095625 0.02841547 0.13435548 0.31244552 0.05396822
AA095542 0.31335517 0.31890594 0.13078863 0.31226555 0.31266575
AA095570 0.08627419 0.14777161 0.32504723 0.08869328 0.08740318 0.32539532
AA095543 0.31404784 0.31944097 0.12723080 0.31335272 0.31400658 0.12441947
AA096029 0.08902335 0.14922636 0.32657999 0.09038502 0.08937366 0.32582974
AA095627 0.08472028 0.14601258 0.32471395 0.08624569 0.08559181 0.32409451
AA095544 0.31193242 0.31684114 0.12879307 0.31012859 0.31165319 0.12388355
AA095634 0.08725959 0.14808463 0.32628736 0.08800230 0.08772173 0.32616434
AA095569 0.06035364 0.13409335 0.31376765 0.06288358 0.05967139 0.31391008
AA095570 AA095543 AA096029 AA095627 AA095544 AA095634
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028
AA095562
AA095623
AA095635
AA095547
AA096030
AA095629
AA095624
AA095637
AA095545
AA095568
AA095625
AA095542
AA095570
AA095543 0.32805086
AA096029 0.04907738 0.32839328
AA095627 0.04110066 0.32652236 0.04966153
AA095544 0.32464949 0.12329120 0.32497694 0.32375252
AA095634 0.04782081 0.32772451 0.05006785 0.04752622 0.32527701
AA095569 0.08853196 0.31518086 0.08998039 0.08654804 0.31173884 0.08800186
$Dgeo
AA095616 AA093614 AA095550 AA095620 AA095553
AA093614 6.174851e+05
AA095550 5.835782e+05 3.391609e+04
AA095620 8.419934e+05 5.960629e+05 5.949874e+05
AA095553 9.798642e+05 3.712245e+05 4.037582e+05 6.231797e+05
AA095548 9.812641e+05 3.728293e+05 4.053365e+05 6.227998e+05 1.916028e+03
AA095617 2.665915e+04 5.962914e+05 5.623756e+05 8.156321e+05 9.570266e+05
AA093615 6.173752e+05 1.211815e+02 3.380511e+04 5.960078e+05 3.713162e+05
AA095626 6.173684e+05 1.279293e+02 3.379828e+04 5.960062e+05 3.713224e+05
AA095636 8.168964e+05 5.934916e+05 5.906269e+05 3.156877e+04 6.391648e+05
AA095546 9.798643e+05 3.712245e+05 4.037583e+05 6.231798e+05 6.285262e-02
AA096028 1.740869e+05 4.953333e+05 4.621578e+05 6.689795e+05 8.400489e+05
AA095562 6.173776e+05 1.188520e+02 3.380748e+04 5.960083e+05 3.713141e+05
AA095623 6.173668e+05 1.294963e+02 3.379670e+04 5.960058e+05 3.713238e+05
AA095635 8.168936e+05 5.934930e+05 5.906280e+05 3.157358e+04 6.391688e+05
AA095547 9.798605e+05 3.712210e+05 4.037547e+05 6.231768e+05 3.875288e+00
AA096030 1.740889e+05 4.953303e+05 4.621548e+05 6.689779e+05 8.400460e+05
AA095629 6.173757e+05 1.206880e+02 3.380561e+04 5.960079e+05 3.713158e+05
AA095624 6.173735e+05 1.228971e+02 3.380337e+04 5.960074e+05 3.713178e+05
AA095637 8.419919e+05 5.960636e+05 5.949879e+05 2.682530e+00 6.231817e+05
AA095545 1.029991e+06 4.221159e+05 4.546300e+05 6.434768e+05 5.089205e+04
AA095568 6.151320e+05 1.589271e+04 3.540922e+04 6.116504e+05 3.782367e+05
AA095625 6.173771e+05 1.193680e+02 3.380695e+04 5.960082e+05 3.713146e+05
AA095542 1.015144e+06 4.088057e+05 4.410892e+05 6.287432e+05 3.881126e+04
AA095570 1.740826e+05 4.953402e+05 4.621647e+05 6.689832e+05 8.400557e+05
AA095543 1.015212e+06 4.088855e+05 4.411675e+05 6.287210e+05 3.890289e+04
AA096029 1.740471e+05 4.954125e+05 4.622372e+05 6.690104e+05 8.401240e+05
AA095627 1.740866e+05 4.953339e+05 4.621584e+05 6.689798e+05 8.400495e+05
AA095544 1.014979e+06 4.086623e+05 4.409426e+05 6.285635e+05 3.870400e+04
AA095634 1.740548e+05 4.954047e+05 4.622294e+05 6.690034e+05 8.401155e+05
AA095569 5.850930e+05 3.239465e+04 1.908246e+03 5.961199e+05 4.025826e+05
AA095548 AA095617 AA093615 AA095626 AA095636
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617 9.584078e+05
AA093615 3.729208e+05 5.961802e+05
AA095626 3.729270e+05 5.961734e+05 6.937866e+00
AA095636 6.388662e+05 7.906359e+05 5.934308e+05 5.934289e+05
AA095546 1.915997e+03 9.570267e+05 3.713163e+05 3.713225e+05 6.391649e+05
AA096028 8.412906e+05 1.474645e+05 4.952148e+05 4.952079e+05 6.444533e+05
AA095562 3.729187e+05 5.961826e+05 2.400323e+00 9.338189e+00 5.934315e+05
AA095623 3.729284e+05 5.961718e+05 8.546075e+00 1.608209e+00 5.934284e+05
AA095635 6.388701e+05 7.906332e+05 5.934322e+05 5.934303e+05 5.104533e+00
AA095547 1.917960e+03 9.570229e+05 3.713128e+05 3.713190e+05 6.391618e+05
AA096030 8.412876e+05 1.474664e+05 4.952118e+05 4.952049e+05 6.444518e+05
AA095629 3.729204e+05 5.961807e+05 5.082852e-01 7.446151e+00 5.934309e+05
AA095624 3.729224e+05 5.961785e+05 1.765922e+00 5.171943e+00 5.934303e+05
AA095637 6.228018e+05 8.156306e+05 5.960084e+05 5.960068e+05 3.156624e+04
AA095545 4.929430e+04 1.007028e+06 4.222076e+05 4.222138e+05 6.613808e+05
AA095568 3.798801e+05 5.943659e+05 1.592592e+04 1.592619e+04 6.088960e+05
AA095625 3.729191e+05 5.961821e+05 1.868420e+00 8.806286e+00 5.934313e+05
AA095542 3.699378e+04 9.920808e+05 4.088955e+05 4.089016e+05 6.463415e+05
AA095570 8.412973e+05 1.474601e+05 4.952217e+05 4.952148e+05 6.444568e+05
AA095543 3.708478e+04 9.921476e+05 4.089752e+05 4.089813e+05 6.463233e+05
AA096029 8.413656e+05 1.474252e+05 4.952940e+05 4.952871e+05 6.444820e+05
AA095627 8.412911e+05 1.474641e+05 4.952154e+05 4.952084e+05 6.444536e+05
AA095544 3.688393e+04 9.919143e+05 4.087520e+05 4.087582e+05 6.461587e+05
AA095634 8.413571e+05 1.474328e+05 4.952861e+05 4.952792e+05 6.444750e+05
AA095569 4.041650e+05 5.639225e+05 3.228544e+04 3.227865e+04 5.918387e+05
AA095546 AA096028 AA095562 AA095623 AA095635
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028 8.400490e+05
AA095562 3.713141e+05 4.952172e+05
AA095623 3.713239e+05 4.952063e+05 1.094640e+01
AA095635 6.391688e+05 6.444507e+05 5.934329e+05 5.934298e+05
AA095547 3.938140e+00 8.400451e+05 3.713106e+05 3.713204e+05 6.391658e+05
AA096030 8.400460e+05 3.014050e+00 4.952142e+05 4.952033e+05 6.444491e+05
AA095629 3.713158e+05 4.952153e+05 1.892038e+00 9.054360e+00 5.934324e+05
AA095624 3.713179e+05 4.952131e+05 4.166246e+00 6.780152e+00 5.934317e+05
AA095637 6.231818e+05 6.689781e+05 5.960089e+05 5.960064e+05 3.157105e+04
AA095545 5.089200e+04 8.889012e+05 4.222055e+05 4.222152e+05 6.613850e+05
AA095568 3.782368e+05 4.965936e+05 1.592582e+04 1.592626e+04 6.088974e+05
AA095625 3.713146e+05 4.952167e+05 5.319035e-01 1.041449e+01 5.934328e+05
AA095542 3.881121e+04 8.733243e+05 4.088934e+05 4.089030e+05 6.463456e+05
AA095570 8.400557e+05 6.861102e+00 4.952241e+05 4.952132e+05 6.444542e+05
AA095543 3.890284e+04 8.733838e+05 4.089731e+05 4.089828e+05 6.463274e+05
AA096029 8.401240e+05 7.992089e+01 4.952964e+05 4.952855e+05 6.444794e+05
AA095627 8.400495e+05 5.364397e-01 4.952178e+05 4.952068e+05 6.444510e+05
AA095544 3.870395e+04 8.731489e+05 4.087499e+05 4.087596e+05 6.461629e+05
AA095634 8.401156e+05 7.277465e+01 4.952885e+05 4.952776e+05 6.444724e+05
AA095569 4.025827e+05 4.639055e+05 3.228779e+04 3.227708e+04 5.918399e+05
AA095547 AA096030 AA095629 AA095624 AA095637
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028
AA095562
AA095623
AA095635
AA095547
AA096030 8.400422e+05
AA095629 3.713123e+05 4.952123e+05
AA095624 3.713143e+05 4.952101e+05 2.274208e+00
AA095637 6.231788e+05 6.689765e+05 5.960085e+05 5.960080e+05
AA095545 5.089550e+04 8.888983e+05 4.222072e+05 4.222092e+05 6.434790e+05
AA095568 3.782334e+05 4.965906e+05 1.592589e+04 1.592599e+04 6.116510e+05
AA095625 3.713111e+05 4.952137e+05 1.360135e+00 3.634342e+00 5.960088e+05
AA095542 3.881413e+04 8.733213e+05 4.088950e+05 4.088970e+05 6.287453e+05
AA095570 8.400519e+05 9.875152e+00 4.952222e+05 4.952199e+05 6.689818e+05
AA095543 3.890576e+04 8.733809e+05 4.089748e+05 4.089768e+05 6.287231e+05
AA096029 8.401202e+05 8.289407e+01 4.952945e+05 4.952922e+05 6.690090e+05
AA095627 8.400456e+05 3.550489e+00 4.952159e+05 4.952136e+05 6.689784e+05
AA095544 3.870686e+04 8.731459e+05 4.087516e+05 4.087536e+05 6.285656e+05
AA095634 8.401117e+05 7.571145e+01 4.952867e+05 4.952844e+05 6.690019e+05
AA095569 4.025791e+05 4.639025e+05 3.228594e+04 3.228371e+04 5.961204e+05
AA095545 AA095568 AA095625 AA095542 AA095570
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028
AA095562
AA095623
AA095635
AA095547
AA096030
AA095629
AA095624
AA095637
AA095545
AA095568 4.291045e+05
AA095625 4.222060e+05 1.592584e+04
AA095542 1.669474e+04 4.161431e+05 4.088938e+05
AA095570 8.889080e+05 4.966005e+05 4.952236e+05 8.733310e+05
AA095543 1.666843e+04 4.162249e+05 4.089736e+05 9.944637e+01 8.733906e+05
AA096029 8.889758e+05 4.966731e+05 4.952959e+05 8.733987e+05 7.316530e+01
AA095627 8.889018e+05 4.965942e+05 4.952172e+05 8.733248e+05 6.324663e+00
AA095544 1.688971e+04 4.160044e+05 4.087504e+05 1.957239e+02 8.731556e+05
AA095634 8.889673e+05 4.966654e+05 4.952880e+05 8.733902e+05 6.611534e+01
AA095569 4.534591e+05 3.353010e+04 3.228727e+04 4.399516e+05 4.639124e+05
AA095543 AA096029 AA095627 AA095544 AA095634
AA093614
AA095550
AA095620
AA095553
AA095548
AA095617
AA093615
AA095626
AA095636
AA095546
AA096028
AA095562
AA095623
AA095635
AA095547
AA096030
AA095629
AA095624
AA095637
AA095545
AA095568
AA095625
AA095542
AA095570
AA095543
AA096029 8.734582e+05
AA095627 8.733844e+05 7.939205e+01
AA095544 2.350750e+02 8.732232e+05 8.731494e+05
AA095634 8.734497e+05 8.635395e+00 7.225263e+01 8.732148e+05
AA095569 4.400301e+05 4.639849e+05 4.639061e+05 4.398054e+05 4.639771e+05
$mantel
Mantel statistic based on Pearson's product-moment correlation
Call:
vegan::mantel(xdis = Dgen, ydis = Dgeo, permutations = permutations, na.rm = TRUE)
Mantel statistic r: 0.5604
Significance: 0.001
Upper quantiles of permutations (null model):
90% 95% 97.5% 99%
0.090 0.119 0.154 0.183
Permutation: free
Number of permutations: 999Multiple linear regression model for within and between populations testing same vs different karyotypes
## reviewer figures -------------------------------------------------------------
# reviewer ibd karyo
review.analysis <- function(gl, analysis = "between"){
if(analysis == "within"){ ndist <- 51; diffCol = "#FFC33B"}
if(analysis == "between"){ ndist <- 1050; diffCol = "#FF5AAF"}
karyoibd <- gl.ibd(gl, distance = "propShared",
paircols = "pop", Dgeo_trans = "Dgeo")
mat <- karyoibd$Dgeo/1000
prop <- karyoibd$Dgen
dfDist <- matrixConvert(mat, c("id1", "id2", "geo"))
dfGen <- matrixConvert(prop, c("id1", "id2", "gen"))
jason2 <- gl
dfkaryo <- jason2@other$ind.metrics[,c("id", "karyo")]
dfpop <- jason2@other$ind.metrics[,c("id", "pop")]
df <- left_join(dfGen, dfDist) %>%
left_join(dfkaryo, by = c("id1" = "id")) %>%
left_join(dfkaryo, by = c("id2" = "id")) %>%
left_join(dfpop, by = c("id1" = "id")) %>%
left_join(dfpop, by = c("id2" = "id")) %>%
mutate(pair = paste(karyo.x,"-", karyo.y)) %>%
filter(geo <= ndist) %>% # change based on question between or within
rowwise() %>%
mutate(karyo = ifelse(karyo.x == karyo.y, "same", "different"),
diffpop = pop.x == pop.y)
indexPost <- c(df$id1, df$id2)
m <- lm(gen ~ geo, data = df)
summary(m)
m2 <- lm(gen ~ geo + karyo, data = df)
summary(m2)
# tab_model(m, m2, show.aic = TRUE, file = "temp.html")
# webshot("temp.html",file = paste0("model_karyo_ibd_", ndist, ".png") ,
# vwidth = 441, vheight = 351)
aic <- AIC(m, m2)
aic$delta <- aic$AIC - min(aic$AIC)
x <- 1:ndist
y1 <- predict(m, newdata = data.frame(geo = x), interval = 'confidence')
y2 <- predict(m2, newdata = data.frame(geo = x, karyo = "same"))
y3 <- predict(m2, newdata = data.frame(geo = x, karyo = "different"))
predmodel <- data.frame(geo = rep(x,2), gen = c(y2, y3),
karyo = rep(c("same", "different"), each = ndist))
sm <- summary(m2)
b0 <- round(m2$coefficients[1],3)
b1 <- signif(m2$coefficients[2], 1)
b2 <- round(m2$coefficients[3], 3)
r2 <- round(sm$r.squared,2)
tb2 <- round(sm$coefficients[3,3], 2)
mExpress <- paste0(b0 ,
" + ", b1, " + ", b2)
pval <- round(sm$coefficients[3,4],2)
reviewerPlot <-ggplot(df, aes(geo, gen, fill = karyo)) +
geom_point(alpha = 0.7, size = 4, pch = 21) +
theme_classic() +
geom_line(data = filter(predmodel, geo < ndist),
aes(x = geo, y = gen, colour = karyo), linewidth = 1, lty = 5)+
xlab("Distance (km)")+
ylab("1-(Proportion of Shared Alleles)")+
scale_fill_manual(values = c(different = diffCol, same = "black"))+
scale_colour_manual(values = c(different = diffCol, same = "black"))+
# theme(legend.position = "none") +
geom_text(aes(x = 39, y = 0.05, label = c("")), cex = 5)+
theme(legend.position = "bottom")+
labs(fill = "Karyotype", colour = "Karyotype")
return(reviewerPlot)
}review.analysis(gl = vac.gl18, analysis = "between")Starting gl.ibd
Analysis performed on the genlight object.
Coordinates transformed to Mercator (google) projection to calculate distances in meters. Coordinates used from: x@other$latlon (Mercator transformed)
Transformation of Dgeo: Dgeo
Genetic distance: propShared
Tranformation of Dgen: Dgen
Mantel statistic based on Pearson's product-moment correlation
Call:
vegan::mantel(xdis = Dgen, ydis = Dgeo, permutations = permutations, na.rm = TRUE)
Mantel statistic r: 0.5604
Significance: 0.001
Upper quantiles of permutations (null model):
90% 95% 97.5% 99%
0.0922 0.1273 0.1537 0.1886
Permutation: free
Number of permutations: 999
Completed: gl.ibd Joining with `by = join_by(id1, id2)`
review.analysis(gl = vac.gl18, analysis = "within")Starting gl.ibd
Analysis performed on the genlight object.
Coordinates transformed to Mercator (google) projection to calculate distances in meters. Coordinates used from: x@other$latlon (Mercator transformed)
Transformation of Dgeo: Dgeo
Genetic distance: propShared
Tranformation of Dgen: Dgen
Mantel statistic based on Pearson's product-moment correlation
Call:
vegan::mantel(xdis = Dgen, ydis = Dgeo, permutations = permutations, na.rm = TRUE)
Mantel statistic r: 0.5604
Significance: 0.001
Upper quantiles of permutations (null model):
90% 95% 97.5% 99%
0.0939 0.1295 0.1625 0.2131
Permutation: free
Number of permutations: 999
Completed: gl.ibd Joining with `by = join_by(id1, id2)`
Characterising a large chromosomal inversion
vac.gl <- gl.load("./data/varanus_MBE_Karyotypes.rds")Starting gl.load
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Loaded object of type SNP from ./data/varanus_MBE_Karyotypes.rds
Completed: gl.load class(vac.gl) <- "dartR"
####Add position for loci metadata
vac.gl@position <- as.integer(runif(nLoc(vac.gl), 2, 49))
# subset SNPs that align to inferred chromosome pool scaffolds -----------------
# how many reads align to flow sorted chromosome pool?
table(vac.gl@other$loc.metrics$Chrom_Varanus_JD_vac_aligned_chr6_7 != "")
FALSE TRUE
283593 17974 # Index those loci
index6 <-
vac.gl@other$loc.metrics$Chrom_Varanus_JD_vac_aligned_chr6_7 != ""
# assign alleles aligned to chromosome 6_7 scaffolds to a new genlight object --
vac.gl6 <- vac.gl[, index6]
gl.smearplot(vac.gl6, group.pop = FALSE) Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Starting gl.smearplot 
Completed: gl.smearplot # add DAPI Karyotype individual metric# report private alleles and fixed alleles per pair of populations for vac.gl6
gl.report.pa(vac.gl6)Starting gl.report.pa
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
p1 p2 pop1 pop2 N1 N2 fixed priv1 priv2 Chao1 Chao2 totalpriv AFD asym
1 1 2 AA MA 5 7 36 298 1213 72 121 1511 0.037 NA
2 1 3 AA MM 5 22 97 274 3973 72 697 4247 0.078 NA
3 2 3 MA MM 7 22 35 310 3346 121 697 3656 0.063 NA
asym.sig
1 NA
2 NA
3 NA
Table of private alleles and fixed differences returned
Completed: gl.report.pa p1 p2 pop1 pop2 N1 N2 fixed priv1 priv2 Chao1 Chao2 totalpriv AFD asym
1 1 2 AA MA 5 7 36 298 1213 72 121 1511 0.037 NA
2 1 3 AA MM 5 22 97 274 3973 72 697 4247 0.078 NA
3 2 3 MA MM 7 22 35 310 3346 121 697 3656 0.063 NA
asym.sig
1 NA
2 NA
3 NA#pop(vac.gl6) <- vac.gl6@other$ind.metrics$DAPI
table(pop(vac.gl6))
AA MA MM
5 7 22 #s <- gl.smearplot(glkaryo, group.pop = TRUE)
pop(vac.gl6) <- vac.gl6@other$ind.metrics$popInvestigate the West only - all three karyotypes with geneflow
### Check the genlight object for dartR requirements
vac.gl6 <- gl.compliance.check(vac.gl6)Starting gl.compliance.check
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Checking coding of SNPs
SNP data scored NA, 0, 1 or 2 confirmed
Checking for population assignments
Population assignments confirmed
Checking locus metrics and flags
Recalculating locus metrics
Checking for monomorphic loci
Dataset contains monomorphic loci
Checking for loci with all missing data
Dataset contains loci with all missing dat
Checking whether individual names are unique.
Checking for individual metrics
Individual metrics confirmed
Spelling of coordinates checked and changed if necessary to
lat/lon
Completed: gl.compliance.check vac.gl6@loc.names %>% duplicated %>% table.
FALSE
17974 # Subset the western population ------------------------------------------------
vac.gl6@other$ind.metrics$ind [1] SW1 bh1 BH9 MI1 CC1 CC10 SW2 bh2 BHA MI2a CC2 BHF RR1 BH3 BHB
[16] MI5 CC3 RR2a bh4 BHC MI4a BH5 BHD CC6 RR3 MI3 CC7 BHJ RR4 RR5
[31] CC8 BHK RR6 BH8
65 Levels: bh1 bh2 BH3 bh4 BH5 BH6 BH7 BH8 BH9 BHA BHB BHC BHD BHE BHF ... zoo2west <- gl.keep.pop(vac.gl6, c("bh"))Starting gl.keep.pop
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Checking for presence of nominated populations
Retaining only populations bh
Warning: Resultant dataset may contain monomorphic loci
Locus metrics not recalculated
Completed: gl.keep.pop # Group individuals of the western population by karyotype
pop(west) <- west@other$ind.metrics$karyo
# Reassign karyotype to a new genlight object ----------------------------------
west <- gl.keep.pop(west, c("AA", "MA", "MM"))Starting gl.keep.pop
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Checking for presence of nominated populations
Retaining only populations AA, MA, MM
Warning: Resultant dataset may contain monomorphic loci
Locus metrics not recalculated
Completed: gl.keep.pop # Report private and fixed alleles for each karyotype
gl.report.pa(west)Starting gl.report.pa
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
p1 p2 pop1 pop2 N1 N2 fixed priv1 priv2 Chao1 Chao2 totalpriv AFD asym
1 1 2 AA MA 5 4 36 416 649 1 2 1065 0.027 NA
2 1 3 AA MM 5 5 146 560 916 1 3 1476 0.043 NA
3 2 3 MA MM 4 5 28 429 599 2 3 1028 0.030 NA
asym.sig
1 NA
2 NA
3 NA
Table of private alleles and fixed differences returned
Completed: gl.report.pa p1 p2 pop1 pop2 N1 N2 fixed priv1 priv2 Chao1 Chao2 totalpriv AFD asym
1 1 2 AA MA 5 4 36 416 649 1 2 1065 0.027 NA
2 1 3 AA MM 5 5 146 560 916 1 3 1476 0.043 NA
3 2 3 MA MM 4 5 28 429 599 2 3 1028 0.030 NA
asym.sig
1 NA
2 NA
3 NA# Add individual metadata to specimen IDs --------------------------------------
pop(west) <-
paste(
west@other$ind.metrics$karyo,
west@other$ind.metrics$id,
west@other$ind.metrics$pop
)
# Fixed difference analysis ----------------------------------------------------
fp6 <- gl.fixed.diff(west)Starting gl.fixed.diff
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Comparing populations for absolute fixed differences
Warning: Monomorphic loci retained, used in calculations
Comparing populations pairwise -- this may take time. Please be patient
Completed: gl.fixed.diff fp6$dfNULLtable(pop(west))
AA AA095569 bh AA AA095623 bh AA AA095625 bh AA AA095626 bh AA AA095629 bh
1 1 1 1 1
MA AA093615 bh MA AA095559 bh MA AA095562 bh MA AA095624 bh MM AA093614 bh
1 1 1 1 1
MM AA095550 bh MM AA095554 bh MM AA095558 bh MM AA095568 bh
1 1 1 1 fp6 <- (gl.fixed.diff(west))Starting gl.fixed.diff
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Comparing populations for absolute fixed differences
Warning: Monomorphic loci retained, used in calculations
Comparing populations pairwise -- this may take time. Please be patient
Completed: gl.fixed.diff # Figure 2 ---------------------------------------------------------------------
res <- as.matrix(gl.fixed.diff(west)$fd)Starting gl.fixed.diff
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Comparing populations for absolute fixed differences
Warning: Monomorphic loci retained, used in calculations
Comparing populations pairwise -- this may take time. Please be patient
Completed: gl.fixed.diff gl.plot.heatmap(res, margins = c(10, 10))Starting gl.plot.heatmap
Processing a data matrix
Starting gl.colors
Selected color type div
Completed: gl.colors 
Completed: gl.plot.heatmap # Table of SNPs per scaffold that align to chromosome 6 ------------------------
table(vac.gl6@other$loc.metrics["Chrom_Varanus_JD_vac_aligned_chr6_7"])Chrom_Varanus_JD_vac_aligned_chr6_7
scaf_162 scaf_174 scaf_178 scaf_18 scaf_185 scaf_44936
0 10084 448 4056 584 1183 849
scaf_44937
770 # Fixed allele analysis for with predicted Karyotypes --------------
pop(vac.gl6) <- vac.gl6@other$ind.metrics$karyo
vac.karyo <- gl.keep.pop(vac.gl6, c("AA", "MA", "MM"))Starting gl.keep.pop
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Checking for presence of nominated populations
Retaining only populations AA, MA, MM
Warning: Resultant dataset may contain monomorphic loci
Locus metrics not recalculated
Completed: gl.keep.pop pop(vac.karyo) <- vac.karyo@other$ind.metrics$karyo
gl.fixed.diff(vac.karyo)Starting gl.fixed.diff
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Comparing populations for absolute fixed differences
Warning: Monomorphic loci retained, used in calculations
Comparing populations pairwise -- this may take time. Please be patient
Completed: gl.fixed.diff $gl
********************
*** DARTR OBJECT ***
********************
** 34 genotypes, 17,974 SNPs , size: 97.4 Mb
missing data: 122942 (=20.12 %) scored as NA
** Genetic data
@gen: list of 34 SNPbin
@ploidy: ploidy of each individual (range: 2-2)
** Additional data
@ind.names: 34 individual labels
@loc.names: 17974 locus labels
@loc.all: 17974 allele labels
@position: integer storing positions of the SNPs [within 69 base sequence]
@pop: population of each individual (group size range: 5-22)
@other: a list containing: loc.metrics, ind.metrics, latlon, loc.metrics.flags, history, verbose
@other$ind.metrics: id, species, ind, pop, sex, lat, lon, e, n, karyo, PCR1, DAPI, FISH
@other$loc.metrics: AlleleID, CloneID, AlleleSequence, TrimmedSequence, Chrom_Komodo_dragon_NCBIv1, ChromPos_Komodo_dragon_NCBIv1, AlnCnt_Komodo_dragon_NCBIv1, AlnEvalue_Komodo_dragon_NCBIv1, Chrom_Varanus_JD_infer_z, ChromPos_Varanus_JD_infer_z, AlnCnt_Varanus_JD_infer_z, AlnEvalue_Varanus_JD_infer_z, Chrom_Varanus_JD_vac_aligned_chr6_7, ChromPos_Varanus_JD_vac_aligned_chr6_7, AlnCnt_Varanus_JD_vac_aligned_chr6_7, AlnEvalue_Varanus_JD_vac_aligned_chr6_7, Chrom_Varanus_JD_infer_w, ChromPos_Varanus_JD_infer_w, AlnCnt_Varanus_JD_infer_w, AlnEvalue_Varanus_JD_infer_w, SNP, SnpPosition, CallRate, OneRatioRef, OneRatioSnp, FreqHomRef, FreqHomSnp, FreqHets, PICRef, PICSnp, AvgPIC, AvgCountRef, AvgCountSnp, RepAvg, clone, uid, rdepth, maf, monomorphs, OneRatio, PIC
@other$latlon[g]: coordinates for all individuals are attached
$fd
AA MA
MA 36
MM 97 35
$pcfd
AA MA
MA 0
MM 1 0
$nobs
AA MA MM
AA NA 10.8 21.7
MA 10.8 NA 23.3
MM 21.7 23.3 NA
$nloc
AA MA MM
AA NA 16319 16368
MA 16319 NA 17402
MM 16368 17402 NA
$expfpos
[,1] [,2] [,3]
[1,] NA NA NA
[2,] NA NA NA
[3,] NA NA NA
$sdfpos
[,1] [,2] [,3]
[1,] NA NA NA
[2,] NA NA NA
[3,] NA NA NA
$pval
[,1] [,2] [,3]
[1,] NA NA NA
[2,] NA NA NA
[3,] NA NA NA
attr(,"class")
[1] "fd"fpk6.1 <- gl.fixed.diff(vac.karyo)Starting gl.fixed.diff
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Comparing populations for absolute fixed differences
Warning: Monomorphic loci retained, used in calculations
Comparing populations pairwise -- this may take time. Please be patient
Completed: gl.fixed.diff fpk6.1$fd AA MA
MA 36
MM 97 35table(pop(vac.karyo))
AA MA MM
5 7 22 # group individuals by karyotype
pops <- seppop(vac.karyo)
# Identify those loci that are fixed for one allele in AA and opposite allele in
# MM and MA are heterozygotes
themany <- which(((abs(
colMeans(as.matrix(pops$AA), na.rm = TRUE) - colMeans(as.matrix(pops$MM),
na.rm = TRUE)
)) == 2) & colMeans(as.matrix(pops$MA) == 1, na.rm = T))
themany47530186-62-T/G 47510325-33-C/T 47506537-50-C/T 58564194-10-C/T 47530853-13-C/A
2475 2697 2943 3166 3178
58568357-53-C/T 47555226-11-T/A 47526162-36-G/T 58574714-5-C/G 47570599-32-G/C
4530 4876 5019 5086 5407
58564685-25-G/A 58568357-43-C/G 47571057-27-A/G 58568730-8-C/T 47534249-44-C/T
5800 5980 6197 6330 6429
58564990-43-G/C 58568170-47-G/A 47572514-30-T/C 47567360-61-C/G 47562299-15-T/A
7015 7392 7575 8894 8990
47490392-36-G/T 47557237-34-A/G 47539268-39-G/C 47584615-15-C/T 58581892-46-T/C
9300 9569 9614 9880 10097
58581176-56-T/C 58582604-32-G/A 47495246-42-A/G 58555628-11-A/C 58534605-26-C/T
10554 10746 13050 13395 14239
47572698-68-C/T 58548074-61-A/G 58548705-34-G/C 47553573-52-C/T 58552886-50-G/A
14309 14506 14826 14837 15026
58544938-37-C/T 47555650-59-C/T 47553573-53-G/T 47537859-68-G/T 58552335-7-G/A
15518 15526 15564 15699 16020
47553754-35-C/T 58554983-38-A/G 58526779-49-T/C 47495750-16-T/G 58529930-35-G/C
16725 16778 17129 17471 17788 # Supplemenarty Table 5 of SNPs sorted for fixed differences--------------------
vac.karyo@other$loc.metrics$TrimmedSequence[themany] [1] TGCAGCTTTAAGTGTGCAATTGCCACACACTCCAATGCTTGTGTGAACTGACCTTCTCACACTCCACTG
[2] TGCAGATGCTGGGGGTGAATCTGGGCCCTCTTGCCTGCTCCCCAACTTTGCAAGGATGTGGTAGGGATT
[3] TGCAGAACCTCAGACCCACCAGGGAGCCCCAGATGGACACTCACCTCCCCCAAAGCTTCATGCCTTTCT
[4] TGCAGAAAATCGTCATTACCATAGAGGGGGAAAGGCAGCTAAAGGTGAGACAGGAAGGGCCCCGAAAGC
[5] TGCAGGCAAAAATCAAAAATTTCAAGCAAAACAATGAACTGTTTCACACATAATGGCAGGGAAGTGCAG
[6] TGCAGAGAGGGACATGGGGGAAGAATTCCAGCAGCCAGCCAAGCCTGGTATGACTCCTGATCCCATGAT
[7] TGCAGCGGAAATCTTTCAGCAAGGGCCACCCCATTCAATGGCAAAAGCCATGTGACAGACCATTAAACT
[8] TGCAGAAGTGGCGAGGACCAAAATACGGCGATCTTCGTGCCCATACACGCATTTTTAATACCTCAGCTG
[9] TGCAGCGAATGGTCCCTCAGATAAGAGCCTTAAGATGTTCCTGCAAAAGAACATGTGAGCATGAGCGGT
[10] TGCAGAATGAGAAGACCTGGTCTAGTAAATGTGTCATCAAATTCCAGAAAAGTGAAATGAACCATAGTG
[11] TGCAGCAGTGTCAGTAGATTCCACCGGTGCTTCCAACGCATAAAAAAGACAGAAATCACAGGCTATCCT
[12] TGCAGAGAGGGACATGGGGGAAGAATTCCAGCAGCCAGCCAAGCCTGGTATGACTCCTGATCCCATGAT
[13] TGCAGATTTTAAGAAGGAGGGGTTATGAAAGTGGAATGTATCATACAAGTTCTTCTAAGTAAGAGAAAT
[14] TGCAGCGTCGATCCTCCCGGGCATCCCACTCGCCCCGCCAGGCCATTTTGCCACTTCACTCGCCAGCAA
[15] TGCAGTTGCAGTACTAGCGGTAGTTTTTCAATGGGAGATTAAAGCAAGCTTGTTCATTCACATACCGTA
[16] TGCAGCAAACATCATTAACATAGTGCCTGCGGGCTGCTTTAGTGTCTGCTATCGATAGCAGAGACTAAA
[17] TGCAGAAATATGTAGAAATAAAGAAAACCGTATAAAATGATTCTAAAGGTACGATCCTGTACAAGATTA
[18] TGCAGGTGATTACAGCAACCCACCGTAAAATCAGTCTCGGGTTCAGGGAAGGCAACTACTTGGCATGGG
[19] TGCAGGTCCTAACTTCCTGCACTGACACTCTTGCAAAGACCAAGAAAATCCTGATATTCCCCATCCTCT
[20] TGCAGATGAGTTCTGTGATTATGCTCTTTATAGAATGCTCGTTTTCACCATATCAATGCTTCTAGGAGT
[21] TGCAGAAGAAGGTTGCTGGTTTGCACAACAGTAATTGCCTGAGAGTTGGTGGGCTTCCTCTCCGCTCAG
[22] TGCAGTACCTCCACCTGGCATGTATCTTTCTGTCACAATGACTGACAATAGATTGCGGACTGAACGAAG
[23] TGCAGACTTGCTACCCTGTTGAAGTGAATACCTCCCACAGACTCATTGCAAAGACATGGCGACATGCCA
[24] TGCAGACAGAAACTTCCCCTTAGTCACTCTTCGGTCATCGTTTCCCAAGGAGGACCGTTTCCTACCCCT
[25] TGCAGGCGTCTTACACTCCAACAAAGTACTGGGTCCGACGCGATGCTTGATGTCTCGCACGGGCAACTC
[26] TGCAGTTACCATTTCCCCATCCTTATTAACCTCTAGATCAGTTACTGCTTAGGCACTACCCCCCAGTTC
[27] TGCAGACAGAAACTTTCCCTTAGTCACTCTTCGGTCATCGTTTCCCAAGGAGGACCGTTTCCTACCCCT
[28] TGCAGCTGCCTCTATAACCTGTCTAGGCAGCCCTCACAAGACAGACTGGATTCTGCGGAAGAGGCCAAG
[29] TGCAGTCCTGGATTTTAAGTGCCTTTCTTTCTGCTTGAACAGGGAAGGCTTCTGAACCTGGTGAGATCC
[30] TGCAGAGGAGGGTAGGACAGGTTCCACTGGAACCATGCTCAGAGAACCAAGGTTCAATCTGGATGCCAG
[31] TGCAGTATGACACAGTAGAGCAGGAGTCCTTAAACTTTTTCTAAAGGGGGCCAGTTGACAGGTGCCAGC
[32] TGCAGCAGAAAATGCACTAAGAAATGCCACCAGCCAGCCATGCCTCCTCCCAGAACACTCCATTCCACG
[33] TGCAGGTGAGGAACAGGTGAAGAATGGTGGGCAAGTGCTCTTCCAGGGTAGCTTGTCCACATTTACTGA
[34] TGCAGACTGCCACAGAGGAGTTGCAGCTCAACACAAGTGGGATTAGTTTGCACGGCATGAGCGGTTCAG
[35] TGCAGGAGAGTTGCTTGCTTGCTTGTTTTCTGTACCACTCAATAGCCAAGGCTCTCTCGGACTGCTTTA
[36] TGCAGTTACAAGCAAACTGAACAACCAGAAAAGAAAACGTTGACCTAGATGTTTGCTACTCTTACTCAT
[37] TGCAGCTTGCAACCTCTAAAGGGCCGGGTGGTGTGCTCAGGCAGAAGTCCATTCCTTAACGTGAGAATA
[38] TGCAGACTGCCACAGAGGAGTTGCAGCTCAACACAAGTGGGATTAGTTTGCACGGCATGAGCGGTTCAG
[39] TGCAGAACCCTGGGCACTGTCAGCCCAGCCATTGATCTGAACTGTGGTGGCAATGGCCAATTATTCAGG
[40] TGCAGGTGTATTCAGAGTACAGTAGGCTCTCTGTTAACCGGAATTCAAACAACTGGCAAAAATAAAGAA
[41] TGCAGAGCCTGGCCTTAAGATAAACACCTCTGCTTCTCTCATCTCAACCTCTGGAATTGGGCCACATTC
[42] TGCAGCGTCTGCCTGCTGGGTCTCTTGGATTCCTCTGGATAGCTCCAGAGAGCCTCCATCTCTCCCTTC
[43] TGCAGCGCTGTTGTTAGCAAGCAAAACTAGGACAGCTTATGAGTATACGTTAGGCATGAGCGGTTCAGC
[44] TGCAGGAAAGACGGGCTCAATCTCAGCCATTCCCCTGCTAACCAGCATGATCACAGCCATCTCCCCACC
[45] TGCAGAGGGGCTCTAATCTTGATCTGCGCATATCAGGGTTTTTAAAAACAAATATACACTTCGTTGCAT
183938 Levels: TGCAGAAAAAAATCATTAAATTATTCCTGGACTGTACCATTTCCGGGCACAAGTAGAGGGATAAAGGTC ...hits <- vac.karyo@other$loc.metrics[themany, ]
hits AlleleID CloneID
39780 47530186|F|0-62:T>G-62:T>G 47530186
43463 47510325|F|0-33:C>T-33:C>T 47510325
46899 47506537|F|0-50:C>T-50:C>T 47506537
50141 58564194|F|0-10:C>T-10:C>T 58564194
50274 47530853|F|0-13:C>A-13:C>A 47530853
70972 58568357|F|0-53:C>T-53:C>T 58568357
76139 47555226|F|0-11:T>A-11:T>A 47555226
78208 47526162|F|0-36:G>T-36:G>T 47526162
79343 58574714|F|0-5:C>G-5:C>G 58574714
84162 47570599|F|0-32:G>C-32:G>C 47570599
90579 58564685|F|0-25:G>A-25:G>A 58564685
92968 58568357|F|0-43:C>G-43:C>G 58568357
95906 47571057|F|0-27:A>G-27:A>G 47571057
97972 58568730|F|0-8:C>T-8:C>T 58568730
99146 47534249|F|0-44:C>T-44:C>T 47534249
109333 58564990|F|0-43:G>C-43:G>C 58564990
115084 58568170|F|0-47:G>A-47:G>A 58568170
117389 47572514|F|0-30:T>C-30:T>C 47572514
139763 47567360|F|0-61:C>G-61:C>G 47567360
140882 47562299|F|0-15:T>A-15:T>A 47562299
146039 47490392|F|0-36:G>T-36:G>T 47490392
149807 47557237|F|0-34:A>G-34:A>G 47557237
150336 47539268|F|0-39:G>C-39:G>C 47539268
153551 47584615|F|0-15:C>T-15:C>T 47584615
156726 58581892|F|0-46:T>C-46:T>C 58581892
163050 58581176|F|0-56:T>C-56:T>C 58581176
166096 58582604|F|0-32:G>A-32:G>A 58582604
205464 47495246|F|0-42:A>G-42:A>G 47495246
211014 58555628|F|0-11:A>C-11:A>C 58555628
224380 58534605|F|0-26:C>T-26:C>T 58534605
225655 47572698|F|0-68:C>T-68:C>T 47572698
229644 58548074|F|0-61:A>G-61:A>G 58548074
235514 58548705|F|0-34:G>C-34:G>C 58548705
235706 47553573|F|0-52:C>T-52:C>T 47553573
238914 58552886|F|0-50:G>A-50:G>A 58552886
247070 58544938|F|0-37:C>T-37:C>T 58544938
247268 47555650|F|0-59:C>T-59:C>T 47555650
248073 47553573|F|0-53:G>T-53:G>T 47553573
250541 47537859|F|0-68:G>T-68:G>T 47537859
255750 58552335|F|0-7:G>A-7:G>A 58552335
268769 47553754|F|0-35:C>T-35:C>T 47553754
269844 58554983|F|0-38:A>G-38:A>G 58554983
277181 58526779|F|0-49:T>C-49:T>C 58526779
283756 47495750|F|0-16:T>G-16:T>G 47495750
295061 58529930|F|0-35:G>C-35:G>C 58529930
AlleleSequence
39780 TGCAGCTTTAAGTGTGCAATTGCCACACACTCCAATGCTTGTGTGAACTGACCTTCTCACACTCCACTG
43463 TGCAGATGCTGGGGGTGAATCTGGGCCCTCTTGCCTGCTCCCCAACTTTGCAAGGATGTGGTAGGGATT
46899 TGCAGAACCTCAGACCCACCAGGGAGCCCCAGATGGACACTCACCTCCCCCAAAGCTTCATGCCTTTCT
50141 TGCAGAAAATCGTCATTACCATAGAGGGGGAAAGGCAGCTAAAGGTGAGACAGGAAGGGCCCCGAAAGC
50274 TGCAGGCAAAAATCAAAAATTTCAAGCAAAACAATGAACTGTTTCACACATAATGGCAGGGAAGTGCAG
70972 TGCAGAGAGGGACATGGGGGAAGAATTCCAGCAGCCAGCCAAGCCTGGTATGACTCCTGATCCCATGAT
76139 TGCAGCGGAAATCTTTCAGCAAGGGCCACCCCATTCAATGGCAAAAGCCATGTGACAGACCATTAAACT
78208 TGCAGAAGTGGCGAGGACCAAAATACGGCGATCTTCGTGCCCATACACGCATTTTTAATACCTCAGCTG
79343 TGCAGCGAATGGTCCCTCAGATAAGAGCCTTAAGATGTTCCTGCAAAAGAACATGTGAGCATGAGCGGT
84162 TGCAGAATGAGAAGACCTGGTCTAGTAAATGTGTCATCAAATTCCAGAAAAGTGAAATGAACCATAGTG
90579 TGCAGCAGTGTCAGTAGATTCCACCGGTGCTTCCAACGCATAAAAAAGACAGAAATCACAGGCTATCCT
92968 TGCAGAGAGGGACATGGGGGAAGAATTCCAGCAGCCAGCCAAGCCTGGTATGACTCCTGATCCCATGAT
95906 TGCAGATTTTAAGAAGGAGGGGTTATGAAAGTGGAATGTATCATACAAGTTCTTCTAAGTAAGAGAAAT
97972 TGCAGCGTCGATCCTCCCGGGCATCCCACTCGCCCCGCCAGGCCATTTTGCCACTTCACTCGCCAGCAA
99146 TGCAGTTGCAGTACTAGCGGTAGTTTTTCAATGGGAGATTAAAGCAAGCTTGTTCATTCACATACCGTA
109333 TGCAGCAAACATCATTAACATAGTGCCTGCGGGCTGCTTTAGTGTCTGCTATCGATAGCAGAGACTAAA
115084 TGCAGAAATATGTAGAAATAAAGAAAACCGTATAAAATGATTCTAAAGGTACGATCCTGTACAAGATTA
117389 TGCAGGTGATTACAGCAACCCACCGTAAAATCAGTCTCGGGTTCAGGGAAGGCAACTACTTGGCATGGG
139763 TGCAGGTCCTAACTTCCTGCACTGACACTCTTGCAAAGACCAAGAAAATCCTGATATTCCCCATCCTCT
140882 TGCAGATGAGTTCTGTGATTATGCTCTTTATAGAATGCTCGTTTTCACCATATCAATGCTTCTAGGAGT
146039 TGCAGAAGAAGGTTGCTGGTTTGCACAACAGTAATTGCCTGAGAGTTGGTGGGCTTCCTCTCCGCTCAG
149807 TGCAGTACCTCCACCTGGCATGTATCTTTCTGTCACAATGACTGACAATAGATTGCGGACTGAACGAAG
150336 TGCAGACTTGCTACCCTGTTGAAGTGAATACCTCCCACAGACTCATTGCAAAGACATGGCGACATGCCA
153551 TGCAGACAGAAACTTCCCCTTAGTCACTCTTCGGTCATCGTTTCCCAAGGAGGACCGTTTCCTACCCCT
156726 TGCAGGCGTCTTACACTCCAACAAAGTACTGGGTCCGACGCGATGCTTGATGTCTCGCACGGGCAACTC
163050 TGCAGTTACCATTTCCCCATCCTTATTAACCTCTAGATCAGTTACTGCTTAGGCACTACCCCCCAGTTC
166096 TGCAGACAGAAACTTTCCCTTAGTCACTCTTCGGTCATCGTTTCCCAAGGAGGACCGTTTCCTACCCCT
205464 TGCAGCTGCCTCTATAACCTGTCTAGGCAGCCCTCACAAGACAGACTGGATTCTGCGGAAGAGGCCAAG
211014 TGCAGTCCTGGATTTTAAGTGCCTTTCTTTCTGCTTGAACAGGGAAGGCTTCTGAACCTGGTGAGATCC
224380 TGCAGAGGAGGGTAGGACAGGTTCCACTGGAACCATGCTCAGAGAACCAAGGTTCAATCTGGATGCCAG
225655 TGCAGTATGACACAGTAGAGCAGGAGTCCTTAAACTTTTTCTAAAGGGGGCCAGTTGACAGGTGCCAGC
229644 TGCAGCAGAAAATGCACTAAGAAATGCCACCAGCCAGCCATGCCTCCTCCCAGAACACTCCATTCCACG
235514 TGCAGGTGAGGAACAGGTGAAGAATGGTGGGCAAGTGCTCTTCCAGGGTAGCTTGTCCACATTTACTGA
235706 TGCAGACTGCCACAGAGGAGTTGCAGCTCAACACAAGTGGGATTAGTTTGCACGGCATGAGCGGTTCAG
238914 TGCAGGAGAGTTGCTTGCTTGCTTGTTTTCTGTACCACTCAATAGCCAAGGCTCTCTCGGACTGCTTTA
247070 TGCAGTTACAAGCAAACTGAACAACCAGAAAAGAAAACGTTGACCTAGATGTTTGCTACTCTTACTCAT
247268 TGCAGCTTGCAACCTCTAAAGGGCCGGGTGGTGTGCTCAGGCAGAAGTCCATTCCTTAACGTGAGAATA
248073 TGCAGACTGCCACAGAGGAGTTGCAGCTCAACACAAGTGGGATTAGTTTGCACGGCATGAGCGGTTCAG
250541 TGCAGAACCCTGGGCACTGTCAGCCCAGCCATTGATCTGAACTGTGGTGGCAATGGCCAATTATTCAGG
255750 TGCAGGTGTATTCAGAGTACAGTAGGCTCTCTGTTAACCGGAATTCAAACAACTGGCAAAAATAAAGAA
268769 TGCAGAGCCTGGCCTTAAGATAAACACCTCTGCTTCTCTCATCTCAACCTCTGGAATTGGGCCACATTC
269844 TGCAGCGTCTGCCTGCTGGGTCTCTTGGATTCCTCTGGATAGCTCCAGAGAGCCTCCATCTCTCCCTTC
277181 TGCAGCGCTGTTGTTAGCAAGCAAAACTAGGACAGCTTATGAGTATACGTTAGGCATGAGCGGTTCAGC
283756 TGCAGGAAAGACGGGCTCAATCTCAGCCATTCCCCTGCTAACCAGCATGATCACAGCCATCTCCCCACC
295061 TGCAGAGGGGCTCTAATCTTGATCTGCGCATATCAGGGTTTTTAAAAACAAATATACACTTCGTTGCAT
TrimmedSequence
39780 TGCAGCTTTAAGTGTGCAATTGCCACACACTCCAATGCTTGTGTGAACTGACCTTCTCACACTCCACTG
43463 TGCAGATGCTGGGGGTGAATCTGGGCCCTCTTGCCTGCTCCCCAACTTTGCAAGGATGTGGTAGGGATT
46899 TGCAGAACCTCAGACCCACCAGGGAGCCCCAGATGGACACTCACCTCCCCCAAAGCTTCATGCCTTTCT
50141 TGCAGAAAATCGTCATTACCATAGAGGGGGAAAGGCAGCTAAAGGTGAGACAGGAAGGGCCCCGAAAGC
50274 TGCAGGCAAAAATCAAAAATTTCAAGCAAAACAATGAACTGTTTCACACATAATGGCAGGGAAGTGCAG
70972 TGCAGAGAGGGACATGGGGGAAGAATTCCAGCAGCCAGCCAAGCCTGGTATGACTCCTGATCCCATGAT
76139 TGCAGCGGAAATCTTTCAGCAAGGGCCACCCCATTCAATGGCAAAAGCCATGTGACAGACCATTAAACT
78208 TGCAGAAGTGGCGAGGACCAAAATACGGCGATCTTCGTGCCCATACACGCATTTTTAATACCTCAGCTG
79343 TGCAGCGAATGGTCCCTCAGATAAGAGCCTTAAGATGTTCCTGCAAAAGAACATGTGAGCATGAGCGGT
84162 TGCAGAATGAGAAGACCTGGTCTAGTAAATGTGTCATCAAATTCCAGAAAAGTGAAATGAACCATAGTG
90579 TGCAGCAGTGTCAGTAGATTCCACCGGTGCTTCCAACGCATAAAAAAGACAGAAATCACAGGCTATCCT
92968 TGCAGAGAGGGACATGGGGGAAGAATTCCAGCAGCCAGCCAAGCCTGGTATGACTCCTGATCCCATGAT
95906 TGCAGATTTTAAGAAGGAGGGGTTATGAAAGTGGAATGTATCATACAAGTTCTTCTAAGTAAGAGAAAT
97972 TGCAGCGTCGATCCTCCCGGGCATCCCACTCGCCCCGCCAGGCCATTTTGCCACTTCACTCGCCAGCAA
99146 TGCAGTTGCAGTACTAGCGGTAGTTTTTCAATGGGAGATTAAAGCAAGCTTGTTCATTCACATACCGTA
109333 TGCAGCAAACATCATTAACATAGTGCCTGCGGGCTGCTTTAGTGTCTGCTATCGATAGCAGAGACTAAA
115084 TGCAGAAATATGTAGAAATAAAGAAAACCGTATAAAATGATTCTAAAGGTACGATCCTGTACAAGATTA
117389 TGCAGGTGATTACAGCAACCCACCGTAAAATCAGTCTCGGGTTCAGGGAAGGCAACTACTTGGCATGGG
139763 TGCAGGTCCTAACTTCCTGCACTGACACTCTTGCAAAGACCAAGAAAATCCTGATATTCCCCATCCTCT
140882 TGCAGATGAGTTCTGTGATTATGCTCTTTATAGAATGCTCGTTTTCACCATATCAATGCTTCTAGGAGT
146039 TGCAGAAGAAGGTTGCTGGTTTGCACAACAGTAATTGCCTGAGAGTTGGTGGGCTTCCTCTCCGCTCAG
149807 TGCAGTACCTCCACCTGGCATGTATCTTTCTGTCACAATGACTGACAATAGATTGCGGACTGAACGAAG
150336 TGCAGACTTGCTACCCTGTTGAAGTGAATACCTCCCACAGACTCATTGCAAAGACATGGCGACATGCCA
153551 TGCAGACAGAAACTTCCCCTTAGTCACTCTTCGGTCATCGTTTCCCAAGGAGGACCGTTTCCTACCCCT
156726 TGCAGGCGTCTTACACTCCAACAAAGTACTGGGTCCGACGCGATGCTTGATGTCTCGCACGGGCAACTC
163050 TGCAGTTACCATTTCCCCATCCTTATTAACCTCTAGATCAGTTACTGCTTAGGCACTACCCCCCAGTTC
166096 TGCAGACAGAAACTTTCCCTTAGTCACTCTTCGGTCATCGTTTCCCAAGGAGGACCGTTTCCTACCCCT
205464 TGCAGCTGCCTCTATAACCTGTCTAGGCAGCCCTCACAAGACAGACTGGATTCTGCGGAAGAGGCCAAG
211014 TGCAGTCCTGGATTTTAAGTGCCTTTCTTTCTGCTTGAACAGGGAAGGCTTCTGAACCTGGTGAGATCC
224380 TGCAGAGGAGGGTAGGACAGGTTCCACTGGAACCATGCTCAGAGAACCAAGGTTCAATCTGGATGCCAG
225655 TGCAGTATGACACAGTAGAGCAGGAGTCCTTAAACTTTTTCTAAAGGGGGCCAGTTGACAGGTGCCAGC
229644 TGCAGCAGAAAATGCACTAAGAAATGCCACCAGCCAGCCATGCCTCCTCCCAGAACACTCCATTCCACG
235514 TGCAGGTGAGGAACAGGTGAAGAATGGTGGGCAAGTGCTCTTCCAGGGTAGCTTGTCCACATTTACTGA
235706 TGCAGACTGCCACAGAGGAGTTGCAGCTCAACACAAGTGGGATTAGTTTGCACGGCATGAGCGGTTCAG
238914 TGCAGGAGAGTTGCTTGCTTGCTTGTTTTCTGTACCACTCAATAGCCAAGGCTCTCTCGGACTGCTTTA
247070 TGCAGTTACAAGCAAACTGAACAACCAGAAAAGAAAACGTTGACCTAGATGTTTGCTACTCTTACTCAT
247268 TGCAGCTTGCAACCTCTAAAGGGCCGGGTGGTGTGCTCAGGCAGAAGTCCATTCCTTAACGTGAGAATA
248073 TGCAGACTGCCACAGAGGAGTTGCAGCTCAACACAAGTGGGATTAGTTTGCACGGCATGAGCGGTTCAG
250541 TGCAGAACCCTGGGCACTGTCAGCCCAGCCATTGATCTGAACTGTGGTGGCAATGGCCAATTATTCAGG
255750 TGCAGGTGTATTCAGAGTACAGTAGGCTCTCTGTTAACCGGAATTCAAACAACTGGCAAAAATAAAGAA
268769 TGCAGAGCCTGGCCTTAAGATAAACACCTCTGCTTCTCTCATCTCAACCTCTGGAATTGGGCCACATTC
269844 TGCAGCGTCTGCCTGCTGGGTCTCTTGGATTCCTCTGGATAGCTCCAGAGAGCCTCCATCTCTCCCTTC
277181 TGCAGCGCTGTTGTTAGCAAGCAAAACTAGGACAGCTTATGAGTATACGTTAGGCATGAGCGGTTCAGC
283756 TGCAGGAAAGACGGGCTCAATCTCAGCCATTCCCCTGCTAACCAGCATGATCACAGCCATCTCCCCACC
295061 TGCAGAGGGGCTCTAATCTTGATCTGCGCATATCAGGGTTTTTAAAAACAAATATACACTTCGTTGCAT
Chrom_Komodo_dragon_NCBIv1 ChromPos_Komodo_dragon_NCBIv1
39780 SJPD01000043.1_scaffold34_1 6324171
43463 SJPD01000031.1_scaffold24 16405804
46899 SJPD01000043.1_scaffold34_1 375374
50141 0
50274 SJPD01000031.1_scaffold24 11788603
70972 SJPD01000043.1_scaffold34_1 4580642
76139 SJPD01000043.1_scaffold34_1 7862835
78208 SJPD01000043.1_scaffold34_1 7938504
79343 SJPD01000031.1_scaffold24 10159958
84162 0
90579 0
92968 SJPD01000043.1_scaffold34_1 4580642
95906 0
97972 SJPD01000043.1_scaffold34_1 8699162
99146 SJPD01000031.1_scaffold24 7573219
109333 SJPD01000011.1_scaffold8 35951871
115084 0
117389 0
139763 SJPD01000031.1_scaffold24 10990793
140882 SJPD01000043.1_scaffold34_1 1337171
146039 SJPD01000031.1_scaffold24 10187800
149807 0
150336 SJPD01000031.1_scaffold24 16184650
153551 SJPD01000043.1_scaffold34_1 6564774
156726 0
163050 SJPD01000043.1_scaffold34_1 5237185
166096 0
205464 SJPD01000043.1_scaffold34_1 5621116
211014 0
224380 SJPD01000001.1_scaffold1 114327324
225655 SJPD01000031.1_scaffold24 12436780
229644 SJPD01000043.1_scaffold34_1 8251535
235514 SJPD01000031.1_scaffold24 17012576
235706 0
238914 SJPD01000031.1_scaffold24 8349203
247070 SJPD01000043.1_scaffold34_1 2154387
247268 SJPD01000001.1_scaffold1 113487419
248073 0
250541 SJPD01000031.1_scaffold24 17827486
255750 SJPD01000043.1_scaffold34_1 7881951
268769 SJPD01000031.1_scaffold24 16078793
269844 0
277181 SJPD01000031.1_scaffold24 12273432
283756 SJPD01000003.1_scaffold3 20807026
295061 0
AlnCnt_Komodo_dragon_NCBIv1 AlnEvalue_Komodo_dragon_NCBIv1
39780 1 2.21e-21
43463 1 1.32e-23
46899 1 2.19e-26
50141 0 9.99e+02
50274 1 2.84e-25
70972 2 1.32e-23
76139 1 2.84e-25
78208 1 2.84e-25
79343 1 6.14e-22
84162 0 9.99e+02
90579 0 9.99e+02
92968 2 1.32e-23
95906 0 9.99e+02
97972 1 3.67e-24
99146 1 1.71e-22
109333 10 1.33e-18
115084 0 9.99e+02
117389 0 9.99e+02
139763 1 6.10e-27
140882 1 2.84e-25
146039 1 3.70e-19
149807 0 9.99e+02
150336 1 1.71e-22
153551 1 6.14e-22
156726 0 9.99e+02
163050 1 6.14e-22
166096 0 9.99e+02
205464 1 1.33e-18
211014 0 9.99e+02
224380 1 4.78e-18
225655 1 6.10e-27
229644 1 3.72e-14
235514 1 7.89e-26
235706 0 9.99e+02
238914 1 6.10e-27
247070 1 6.10e-27
247268 1 6.10e-27
248073 0 9.99e+02
250541 1 2.84e-25
255750 1 6.10e-27
268769 1 6.10e-27
269844 0 9.99e+02
277181 1 8.00e-16
283756 1 6.14e-22
295061 0 9.99e+02
Chrom_Varanus_JD_infer_z ChromPos_Varanus_JD_infer_z
39780 0
43463 0
46899 0
50141 0
50274 0
70972 0
76139 0
78208 0
79343 0
84162 0
90579 0
92968 0
95906 0
97972 0
99146 0
109333 0
115084 0
117389 0
139763 0
140882 0
146039 0
149807 0
150336 0
153551 0
156726 0
163050 0
166096 0
205464 0
211014 0
224380 0
225655 0
229644 0
235514 0
235706 0
238914 0
247070 0
247268 0
248073 0
250541 0
255750 0
268769 0
269844 0
277181 0
283756 0
295061 0
AlnCnt_Varanus_JD_infer_z AlnEvalue_Varanus_JD_infer_z
39780 0 999
43463 0 999
46899 0 999
50141 0 999
50274 0 999
70972 0 999
76139 0 999
78208 0 999
79343 0 999
84162 0 999
90579 0 999
92968 0 999
95906 0 999
97972 0 999
99146 0 999
109333 0 999
115084 0 999
117389 0 999
139763 0 999
140882 0 999
146039 0 999
149807 0 999
150336 0 999
153551 0 999
156726 0 999
163050 0 999
166096 0 999
205464 0 999
211014 0 999
224380 0 999
225655 0 999
229644 0 999
235514 0 999
235706 0 999
238914 0 999
247070 0 999
247268 0 999
248073 0 999
250541 0 999
255750 0 999
268769 0 999
269844 0 999
277181 0 999
283756 0 999
295061 0 999
Chrom_Varanus_JD_vac_aligned_chr6_7
39780 scaf_185
43463 scaf_44937
46899 scaf_174
50141 scaf_44937
50274 scaf_178
70972 scaf_44936
76139 scaf_185
78208 scaf_185
79343 scaf_178
84162 scaf_178
90579 scaf_178
92968 scaf_44936
95906 scaf_44936
97972 scaf_185
99146 scaf_178
109333 scaf_178
115084 scaf_178
117389 scaf_185
139763 scaf_178
140882 scaf_174
146039 scaf_178
149807 scaf_178
150336 scaf_44937
153551 scaf_185
156726 scaf_185
163050 scaf_44936
166096 scaf_185
205464 scaf_185
211014 scaf_185
224380 scaf_178
225655 scaf_178
229644 scaf_185
235514 scaf_44937
235706 scaf_178
238914 scaf_178
247070 scaf_174
247268 scaf_178
248073 scaf_178
250541 scaf_44937
255750 scaf_185
268769 scaf_44937
269844 scaf_174
277181 scaf_178
283756 scaf_162
295061 scaf_44936
ChromPos_Varanus_JD_vac_aligned_chr6_7
39780 4535602
43463 1879053
46899 422662
50141 3057519
50274 17533506
70972 2239338
76139 3058006
78208 2982377
79343 15921589
84162 9531917
90579 8627028
92968 2239338
95906 626638
97972 2280435
99146 13361437
109333 16092795
115084 4799684
117389 3789392
139763 16744777
140882 1374442
146039 15947400
149807 12871115
150336 1656795
153551 4311211
156726 1611346
163050 2878581
166096 4311211
205464 5197021
211014 4008715
224380 959068
225655 18176452
229644 2688663
235514 2488100
235706 14281639
238914 14121110
247070 2162400
247268 1932940
248073 14281639
250541 3299754
255750 3038917
268769 1552585
269844 2162466
277181 18014400
283756 27088034
295061 2382323
AlnCnt_Varanus_JD_vac_aligned_chr6_7
39780 1
43463 1
46899 1
50141 1
50274 1
70972 1
76139 1
78208 1
79343 1
84162 1
90579 1
92968 1
95906 1
97972 1
99146 1
109333 6
115084 1
117389 1
139763 1
140882 1
146039 1
149807 1
150336 1
153551 1
156726 1
163050 1
166096 1
205464 1
211014 1
224380 1
225655 2
229644 1
235514 1
235706 1
238914 1
247070 1
247268 1
248073 1
250541 1
255750 1
268769 1
269844 1
277181 1
283756 2
295061 1
AlnEvalue_Varanus_JD_vac_aligned_chr6_7 Chrom_Varanus_JD_infer_w
39780 7.96e-30
43463 7.96e-30
46899 7.96e-30
50141 7.96e-30
50274 7.96e-30
70972 7.96e-30
76139 7.96e-30
78208 7.96e-30
79343 2.88e-24
84162 7.96e-30
90579 7.96e-30
92968 7.96e-30
95906 7.96e-30
97972 7.96e-30
99146 3.70e-28
109333 3.70e-28
115084 3.70e-28
117389 3.70e-28
139763 7.96e-30
140882 7.96e-30
146039 7.96e-30
149807 3.70e-28
150336 7.96e-30
153551 7.96e-30
156726 7.96e-30
163050 8.02e-25
166096 3.70e-28
205464 3.70e-28
211014 3.70e-28
224380 7.96e-30
225655 7.96e-30
229644 7.96e-30
235514 7.96e-30
235706 2.88e-24
238914 7.96e-30
247070 7.96e-30
247268 7.96e-30
248073 2.88e-24
250541 7.96e-30
255750 7.96e-30
268769 7.96e-30
269844 3.70e-28
277181 2.25e-20
283756 2.93e-14
295061 2.25e-20
ChromPos_Varanus_JD_infer_w AlnCnt_Varanus_JD_infer_w
39780 0 0
43463 0 0
46899 0 0
50141 0 0
50274 0 0
70972 0 0
76139 0 0
78208 0 0
79343 0 0
84162 0 0
90579 0 0
92968 0 0
95906 0 0
97972 0 0
99146 0 0
109333 0 0
115084 0 0
117389 0 0
139763 0 0
140882 0 0
146039 0 0
149807 0 0
150336 0 0
153551 0 0
156726 0 0
163050 0 0
166096 0 0
205464 0 0
211014 0 0
224380 0 0
225655 0 0
229644 0 0
235514 0 0
235706 0 0
238914 0 0
247070 0 0
247268 0 0
248073 0 0
250541 0 0
255750 0 0
268769 0 0
269844 0 0
277181 0 0
283756 0 0
295061 0 0
AlnEvalue_Varanus_JD_infer_w SNP SnpPosition CallRate OneRatioRef
39780 999 62:T>G 62 1.000000 0.8529412
43463 999 33:C>T 33 0.970588 0.8484848
46899 999 50:C>T 50 0.823529 0.7500000
50141 999 10:C>T 10 0.852941 0.8275862
50274 999 13:C>A 13 1.000000 0.8529412
70972 999 53:C>T 53 0.823529 0.8571429
76139 999 11:T>A 11 0.941176 0.8437500
78208 999 36:G>T 36 0.794118 0.8148148
79343 999 5:C>G 5 0.735294 0.8000000
84162 999 32:G>C 32 0.941176 0.8437500
90579 999 25:G>A 25 0.735294 0.8000000
92968 999 43:C>G 43 0.823529 0.8571429
95906 999 27:A>G 27 0.823529 0.8214286
97972 999 8:C>T 8 0.941176 0.8437500
99146 999 44:C>T 44 0.823529 0.4285714
109333 999 43:G>C 43 0.823529 0.7857143
115084 999 47:G>A 47 0.323529 0.3636364
117389 999 30:T>C 30 0.588235 0.6000000
139763 999 61:C>G 61 1.000000 0.8529412
140882 999 15:T>A 15 1.000000 0.8529412
146039 999 36:G>T 36 1.000000 0.8529412
149807 999 34:A>G 34 0.735294 0.6400000
150336 999 39:G>C 39 0.794118 0.8148148
153551 999 15:C>T 15 0.764706 0.6153846
156726 999 46:T>C 46 0.735294 0.6800000
163050 999 56:T>C 56 0.558824 0.4210526
166096 999 32:G>A 32 0.411765 0.8571429
205464 999 42:A>G 42 0.970588 0.3333333
211014 999 11:A>C 11 0.911765 0.2903226
224380 999 26:C>T 26 0.794118 0.8148148
225655 999 68:C>T 68 0.852941 0.7931034
229644 999 61:A>G 61 0.941176 0.8125000
235514 999 34:G>C 34 0.970588 0.7575758
235706 999 52:C>T 52 0.911765 0.8709677
238914 999 50:G>A 50 0.823529 0.8214286
247070 999 37:C>T 37 0.823529 0.7857143
247268 999 59:C>T 59 0.882353 0.8333333
248073 999 53:G>T 53 0.941176 0.8437500
250541 999 68:G>T 68 0.941176 0.8750000
255750 999 7:G>A 7 0.823529 0.6428571
268769 999 35:C>T 35 0.852941 0.9310345
269844 999 38:A>G 38 0.735294 0.6800000
277181 999 49:T>C 49 0.588235 0.4500000
283756 999 16:T>G 16 0.352941 0.5000000
295061 999 35:G>C 35 0.382353 0.8461538
OneRatioSnp FreqHomRef FreqHomSnp FreqHets PICRef PICSnp
39780 0.3529412 0.6470588 0.14705882 0.20588235 0.2508651 0.4567474
43463 0.3636364 0.6363636 0.15151515 0.21212121 0.2571166 0.4628099
46899 0.4285714 0.5714286 0.25000000 0.17857143 0.3750000 0.4897959
50141 0.3103448 0.6896552 0.17241379 0.13793103 0.2853746 0.4280618
50274 0.2647059 0.7352941 0.14705882 0.11764706 0.2508651 0.3892734
70972 0.2142857 0.7857143 0.14285714 0.07142857 0.2448980 0.3367347
76139 0.2500000 0.7500000 0.15625000 0.09375000 0.2636719 0.3750000
78208 0.2962963 0.7037037 0.18518519 0.11111111 0.3017833 0.4170096
79343 0.4000000 0.6000000 0.20000000 0.20000000 0.3200000 0.4800000
84162 0.3750000 0.6250000 0.15625000 0.21875000 0.2636719 0.4687500
90579 0.3600000 0.6400000 0.20000000 0.16000000 0.3200000 0.4608000
92968 0.2500000 0.7500000 0.14285714 0.10714286 0.2448980 0.3750000
95906 0.2857143 0.7142857 0.17857143 0.10714286 0.2933673 0.4081633
97972 0.3125000 0.6875000 0.15625000 0.15625000 0.2636719 0.4296875
99146 0.8214286 0.1785714 0.57142857 0.25000000 0.4897959 0.2933673
109333 0.3214286 0.6785714 0.21428571 0.10714286 0.3367347 0.4362245
115084 0.7272727 0.2727273 0.63636364 0.09090909 0.4628099 0.3966942
117389 0.5500000 0.4500000 0.40000000 0.15000000 0.4800000 0.4950000
139763 0.3235294 0.6764706 0.14705882 0.17647059 0.2508651 0.4377163
140882 0.2058824 0.7941176 0.14705882 0.05882353 0.2508651 0.3269896
146039 0.2941176 0.7058824 0.14705882 0.14705882 0.2508651 0.4152249
149807 0.4800000 0.5200000 0.36000000 0.12000000 0.4608000 0.4992000
150336 0.3333333 0.6666667 0.18518519 0.14814815 0.3017833 0.4444444
153551 0.4615385 0.5384615 0.38461538 0.07692308 0.4733728 0.4970414
156726 0.4400000 0.5600000 0.32000000 0.12000000 0.4352000 0.4928000
163050 0.6315789 0.3684211 0.57894737 0.05263158 0.4875346 0.4653740
166096 0.2142857 0.7857143 0.14285714 0.07142857 0.2448980 0.3367347
205464 0.7878788 0.2121212 0.66666667 0.12121212 0.4444444 0.3342516
211014 0.8064516 0.1935484 0.70967742 0.09677419 0.4120708 0.3121748
224380 0.4074074 0.5925926 0.18518519 0.22222222 0.3017833 0.4828532
225655 0.3793103 0.6206897 0.20689655 0.17241379 0.3281807 0.4708680
229644 0.2812500 0.7187500 0.18750000 0.09375000 0.3046875 0.4042969
235514 0.3636364 0.6363636 0.24242424 0.12121212 0.3673095 0.4628099
235706 0.1612903 0.8387097 0.12903226 0.03225806 0.2247659 0.2705515
238914 0.4285714 0.5714286 0.17857143 0.25000000 0.2933673 0.4897959
247070 0.3928571 0.6071429 0.21428571 0.17857143 0.3367347 0.4770408
247268 0.4000000 0.6000000 0.16666667 0.23333333 0.2777778 0.4800000
248073 0.2812500 0.7187500 0.15625000 0.12500000 0.2636719 0.4042969
250541 0.2500000 0.7500000 0.12500000 0.12500000 0.2187500 0.3750000
255750 0.3928571 0.6071429 0.35714286 0.03571429 0.4591837 0.4770408
268769 0.1724138 0.8275862 0.06896552 0.10344828 0.1284185 0.2853746
269844 0.4000000 0.6000000 0.32000000 0.08000000 0.4352000 0.4800000
277181 0.6500000 0.3500000 0.55000000 0.10000000 0.4950000 0.4550000
283756 0.5833333 0.4166667 0.50000000 0.08333333 0.5000000 0.4861111
295061 0.2307692 0.7692308 0.15384615 0.07692308 0.2603550 0.3550296
AvgPIC AvgCountRef AvgCountSnp RepAvg clone uid rdepth
39780 0.3538062 6.39256 5.26549 0.992308 47530186 47530186-62 7.3
43463 0.3599633 6.98502 5.53659 0.992188 47510325 47510325-33 8.0
46899 0.4323980 3.43028 3.11765 0.990741 47506537 47506537-50 3.6
50141 0.3567182 4.65323 3.38182 0.963636 58564194 58564194-10 4.9
50274 0.3200692 5.37970 3.55556 0.991379 47530853 47530853-13 5.5
70972 0.2908163 3.15179 2.61290 0.970588 58568357 58568357-53 3.4
76139 0.3193359 7.28685 6.76923 1.000000 47555226 47555226-11 7.6
78208 0.3593964 9.28947 8.66000 0.991071 47526162 47526162-36 9.8
79343 0.4000000 10.18595 9.39583 1.000000 58574714 58574714-5 11.0
84162 0.3662109 7.08808 5.27273 0.982143 47570599 47570599-32 7.5
90579 0.3904000 3.51101 3.31034 0.980392 58564685 58564685-25 3.7
92968 0.3099490 3.15179 2.68421 0.989583 58568357 58568357-43 3.2
95906 0.3507653 4.36697 3.50000 0.990385 47571057 47571057-27 4.5
97972 0.3466797 3.17225 3.04878 0.959184 58568730 58568730-8 3.5
99146 0.3915816 4.96226 6.76136 0.981818 47534249 47534249-44 7.4
109333 0.3864796 3.43085 3.18182 1.000000 58564990 58564990-43 3.6
115084 0.4297521 5.90370 4.81967 0.987500 58568170 58568170-47 5.9
117389 0.4875000 4.94949 4.31683 1.000000 47572514 47572514-30 5.0
139763 0.3442907 11.39085 9.09804 1.000000 47567360 47567360-61 12.3
140882 0.2889273 12.79012 7.41053 0.992424 47562299 47562299-15 13.1
146039 0.3330450 9.19712 7.79825 0.984127 47490392 47490392-36 10.2
149807 0.4800000 13.12022 9.26087 0.991071 47557237 47557237-34 13.9
150336 0.3731139 16.48000 15.55000 1.000000 47539268 47539268-39 18.1
153551 0.4852071 5.48864 5.31343 0.979167 47584615 47584615-15 5.8
156726 0.4640000 3.57059 3.45714 0.980769 58581892 58581892-46 4.0
163050 0.4764543 14.11538 11.69748 1.000000 58581176 58581176-56 12.4
166096 0.2908163 5.31343 5.20000 0.982143 58582604 58582604-32 5.5
205464 0.3893480 6.20000 6.56981 0.991228 47495246 47495246-42 7.0
211014 0.3621228 4.43333 4.13139 1.000000 58555628 58555628-11 4.3
224380 0.3923182 4.41758 3.63768 0.975410 58534605 58534605-26 4.7
225655 0.3995244 3.65238 2.97059 0.953704 47572698 47572698-68 4.0
229644 0.3544922 3.46185 2.94872 0.956897 58548074 58548074-61 3.6
235514 0.4150597 3.06186 2.65179 0.928571 58548705 58548705-34 3.5
235706 0.2476587 13.40948 9.10769 0.981818 47553573 47553573-52 14.0
238914 0.3915816 4.14583 3.35849 0.981481 58552886 58552886-50 4.5
247070 0.4068878 4.12121 3.25210 0.937500 58544938 58544938-37 4.4
247268 0.3788889 4.54237 3.67442 0.981132 47555650 47555650-59 4.9
248073 0.3339844 13.40948 13.02439 0.990566 47553573 47553573-53 14.7
250541 0.2968750 6.90000 5.63636 1.000000 47537859 47537859-68 7.1
255750 0.4681122 3.20879 2.91304 0.976744 58552335 58552335-7 3.5
268769 0.2068966 6.87374 6.16667 0.988372 47553754 47553754-35 7.0
269844 0.4576000 3.95302 3.07229 0.980392 58554983 58554983-38 4.1
277181 0.4750000 16.03704 9.48322 1.000000 58526779 58526779-49 10.6
283756 0.4930556 6.35000 5.91228 0.983333 47495750 47495750-16 6.3
295061 0.3076923 5.02151 4.66667 0.981481 58529930 58529930-35 5.1
maf monomorphs OneRatio PIC
39780 0.2500 NA NA NA
43463 0.2576 NA NA NA
46899 0.3393 NA NA NA
50141 0.2414 NA NA NA
50274 0.2059 NA NA NA
70972 0.1786 NA NA NA
76139 0.2031 NA NA NA
78208 0.2407 NA NA NA
79343 0.3000 NA NA NA
84162 0.2656 NA NA NA
90579 0.2800 NA NA NA
92968 0.1964 NA NA NA
95906 0.2321 NA NA NA
97972 0.2344 NA NA NA
99146 0.3036 NA NA NA
109333 0.2679 NA NA NA
115084 0.3182 NA NA NA
117389 0.4750 NA NA NA
139763 0.2353 NA NA NA
140882 0.1765 NA NA NA
146039 0.2206 NA NA NA
149807 0.4200 NA NA NA
150336 0.2593 NA NA NA
153551 0.4231 NA NA NA
156726 0.3800 NA NA NA
163050 0.3947 NA NA NA
166096 0.1786 NA NA NA
205464 0.2727 NA NA NA
211014 0.2419 NA NA NA
224380 0.2963 NA NA NA
225655 0.2931 NA NA NA
229644 0.2344 NA NA NA
235514 0.3030 NA NA NA
235706 0.1452 NA NA NA
238914 0.3036 NA NA NA
247070 0.3036 NA NA NA
247268 0.2833 NA NA NA
248073 0.2188 NA NA NA
250541 0.1875 NA NA NA
255750 0.3750 NA NA NA
268769 0.1207 NA NA NA
269844 0.3600 NA NA NA
277181 0.4000 NA NA NA
283756 0.4583 NA NA NA
295061 0.1923 NA NA NAvac.pops <- vac.karyo
# SNPs aligning to scaffolds of interest following fixed allele analysis
table(vac.pops@other$loc.metrics[themany, "Chrom_Varanus_JD_vac_aligned_chr6_7"])
scaf_162 scaf_174 scaf_178 scaf_18 scaf_185 scaf_44936
0 1 4 17 0 12 5
scaf_44937
6 # create an index for only those loci on scaf_178-------------------------------
index_178 <- which(vac.pops@other$loc.metrics$Chrom_Varanus_JD_vac_aligned_chr6_7 == "scaf_178")
# check the index to verify genlight object
index_178 [1] 4 14 19 24 42 45 46 47 54 55 62 66
[13] 67 74 78 82 97 104 119 120 122 125 129 132
[25] 141 143 144 155 157 161 174 175 193 194 199 217
[37] 221 228 229 234 239 240 241 246 247 248 262 266
[49] 269 275 276 281 293 294 299 306 307 312 316 320
[61] 330 333 334 335 349 352 363 367 374 381 385 394
[73] 396 406 407 417 430 439 440 441 442 444 445 446
[85] 447 457 484 495 496 498 502 503 507 524 548 551
[97] 562 571 576 578 579 586 610 612 614 617 618 620
[109] 627 628 645 653 661 663 664 665 666 670 671 672
[121] 677 682 684 685 686 687 693 695 696 698 699 701
[133] 702 704 707 708 709 710 711 720 721 722 723 728
[145] 731 732 734 738 743 746 748 750 751 754 757 760
[157] 765 766 768 770 771 776 778 782 784 787 794 799
[169] 827 828 835 839 850 863 864 865 867 868 869 870
[181] 872 879 881 882 883 886 892 893 897 898 900 915
[193] 920 924 929 930 936 937 938 951 952 953 955 959
[205] 963 969 970 971 973 974 975 977 981 990 991 992
[217] 993 1012 1014 1015 1016 1021 1022 1036 1040 1041 1044 1045
[229] 1046 1047 1049 1051 1053 1055 1057 1059 1061 1063 1075 1081
[241] 1082 1089 1092 1105 1108 1111 1121 1129 1139 1140 1141 1146
[253] 1155 1157 1162 1176 1177 1178 1180 1183 1184 1194 1201 1204
[265] 1205 1211 1212 1215 1230 1239 1240 1243 1244 1252 1254 1263
[277] 1265 1266 1268 1269 1270 1283 1290 1291 1292 1294 1295 1297
[289] 1301 1305 1306 1307 1310 1314 1315 1323 1327 1328 1329 1335
[301] 1336 1337 1349 1350 1354 1364 1365 1366 1367 1368 1369 1371
[313] 1375 1379 1383 1393 1395 1402 1404 1406 1411 1413 1414 1418
[325] 1428 1429 1441 1444 1445 1446 1448 1452 1453 1463 1469 1472
[337] 1473 1475 1477 1479 1488 1492 1493 1501 1505 1507 1508 1509
[349] 1511 1515 1531 1536 1537 1545 1546 1549 1561 1562 1579 1580
[361] 1586 1589 1594 1595 1597 1601 1604 1605 1606 1607 1608 1609
[373] 1611 1616 1645 1649 1652 1653 1675 1677 1681 1682 1683 1684
[385] 1691 1696 1698 1705 1717 1718 1719 1720 1743 1748 1750 1763
[397] 1766 1767 1774 1778 1782 1788 1790 1796 1799 1801 1803 1819
[409] 1820 1821 1823 1825 1826 1828 1831 1836 1837 1838 1839 1840
[421] 1848 1857 1858 1862 1863 1866 1874 1876 1882 1883 1884 1891
[433] 1892 1893 1909 1911 1912 1917 1922 1926 1927 1934 1935 1937
[445] 1938 1949 1950 1951 1952 1953 1955 1957 1958 1961 1967 1970
[457] 1974 1979 1980 1981 1982 1994 2003 2005 2017 2021 2022 2024
[469] 2025 2028 2037 2040 2041 2042 2075 2077 2081 2087 2089 2092
[481] 2094 2097 2099 2101 2103 2104 2107 2111 2117 2119 2120 2121
[493] 2125 2126 2130 2133 2147 2148 2165 2175 2182 2186 2195 2198
[505] 2199 2201 2202 2204 2214 2218 2219 2221 2227 2230 2231 2232
[517] 2233 2235 2238 2240 2243 2254 2255 2256 2264 2268 2275 2284
[529] 2292 2295 2312 2315 2316 2317 2326 2333 2334 2340 2341 2342
[541] 2343 2344 2346 2348 2358 2367 2375 2378 2380 2382 2394 2397
[553] 2406 2413 2414 2421 2424 2425 2434 2436 2446 2447 2450 2451
[565] 2452 2454 2457 2458 2459 2467 2468 2470 2474 2476 2478 2484
[577] 2490 2491 2494 2499 2500 2503 2505 2511 2525 2527 2528 2529
[589] 2530 2539 2540 2559 2569 2572 2573 2574 2575 2576 2582 2583
[601] 2586 2587 2589 2590 2593 2596 2597 2599 2602 2609 2618 2626
[613] 2628 2632 2633 2643 2647 2648 2649 2670 2675 2676 2685 2687
[625] 2702 2712 2716 2724 2726 2732 2733 2747 2752 2760 2761 2762
[637] 2763 2764 2766 2798 2802 2806 2808 2812 2813 2828 2832 2837
[649] 2841 2848 2850 2852 2858 2859 2866 2871 2872 2879 2885 2886
[661] 2887 2888 2917 2920 2922 2925 2926 2941 2942 2950 2956 2957
[673] 2963 2986 2996 2999 3002 3006 3016 3025 3028 3029 3030 3031
[685] 3035 3041 3049 3050 3052 3054 3055 3056 3058 3068 3076 3078
[697] 3082 3086 3100 3108 3109 3125 3126 3129 3130 3131 3141 3142
[709] 3143 3144 3147 3154 3159 3161 3167 3168 3171 3172 3175 3176
[721] 3178 3180 3184 3186 3188 3193 3196 3198 3203 3207 3208 3211
[733] 3212 3213 3221 3223 3229 3232 3236 3237 3241 3242 3244 3250
[745] 3257 3263 3267 3273 3275 3276 3293 3299 3301 3307 3315 3317
[757] 3339 3345 3348 3349 3350 3353 3354 3386 3387 3400 3402 3406
[769] 3412 3416 3427 3430 3432 3434 3436 3440 3447 3450 3464 3467
[781] 3473 3495 3498 3499 3512 3514 3515 3522 3524 3528 3533 3537
[793] 3538 3541 3543 3549 3557 3558 3561 3562 3566 3581 3585 3596
[805] 3597 3613 3617 3626 3628 3630 3637 3638 3640 3644 3648 3652
[817] 3653 3654 3655 3657 3659 3665 3670 3677 3686 3689 3691 3695
[829] 3724 3730 3731 3734 3742 3746 3761 3763 3766 3767 3781 3784
[841] 3791 3793 3794 3796 3797 3801 3810 3811 3816 3819 3820 3824
[853] 3828 3829 3833 3834 3837 3839 3843 3847 3851 3852 3854 3863
[865] 3865 3877 3885 3894 3898 3909 3910 3911 3918 3922 3925 3927
[877] 3932 3938 3941 3942 3947 3950 3954 3955 3956 3957 3958 3959
[889] 3967 3973 3980 3981 3983 3985 3986 3987 3992 3994 3999 4000
[901] 4016 4017 4018 4021 4026 4032 4035 4038 4044 4047 4048 4049
[913] 4051 4055 4057 4058 4059 4060 4071 4073 4076 4084 4089 4100
[925] 4101 4103 4107 4111 4113 4124 4125 4127 4128 4133 4136 4137
[937] 4144 4145 4157 4160 4161 4164 4165 4167 4171 4176 4181 4185
[949] 4192 4193 4194 4198 4201 4204 4214 4220 4223 4226 4227 4235
[961] 4239 4248 4249 4250 4255 4261 4267 4274 4281 4283 4284 4292
[973] 4298 4302 4305 4331 4336 4337 4349 4351 4356 4359 4364 4369
[985] 4372 4375 4386 4387 4389 4390 4394 4395 4403 4425 4428 4430
[997] 4439 4440 4442 4445 4450 4455 4457 4459 4460 4461 4466 4467
[1009] 4472 4476 4479 4481 4482 4485 4491 4495 4505 4507 4519 4520
[1021] 4523 4540 4543 4551 4560 4561 4569 4570 4572 4577 4579 4582
[1033] 4583 4589 4590 4591 4593 4595 4606 4611 4616 4626 4629 4639
[1045] 4642 4648 4650 4651 4656 4657 4666 4667 4673 4674 4678 4679
[1057] 4680 4693 4719 4722 4728 4738 4755 4758 4763 4767 4779 4784
[1069] 4790 4793 4795 4800 4808 4812 4813 4837 4838 4840 4841 4846
[1081] 4852 4853 4854 4862 4864 4874 4878 4885 4891 4906 4915 4930
[1093] 4936 4940 4943 4954 4955 4956 4962 4966 4972 4980 4982 5002
[1105] 5003 5004 5005 5007 5009 5015 5020 5027 5029 5036 5044 5046
[1117] 5056 5059 5068 5069 5086 5087 5088 5092 5101 5109 5117 5119
[1129] 5132 5136 5138 5141 5143 5151 5152 5159 5160 5181 5188 5194
[1141] 5204 5215 5218 5226 5228 5240 5242 5244 5255 5269 5270 5271
[1153] 5273 5274 5279 5281 5282 5284 5291 5314 5315 5316 5335 5337
[1165] 5343 5351 5353 5354 5358 5360 5367 5368 5388 5389 5390 5391
[1177] 5397 5405 5406 5407 5413 5414 5419 5437 5440 5441 5446 5450
[1189] 5456 5457 5458 5459 5460 5462 5464 5465 5468 5475 5480 5481
[1201] 5486 5488 5489 5493 5494 5495 5503 5511 5515 5516 5522 5529
[1213] 5534 5536 5538 5541 5551 5552 5553 5568 5574 5578 5579 5581
[1225] 5583 5585 5594 5596 5614 5623 5625 5627 5628 5631 5633 5642
[1237] 5647 5649 5651 5652 5653 5655 5657 5662 5664 5669 5670 5673
[1249] 5675 5679 5689 5691 5698 5703 5704 5717 5718 5724 5727 5728
[1261] 5730 5732 5743 5745 5747 5752 5758 5764 5765 5768 5770 5777
[1273] 5781 5782 5787 5793 5794 5796 5800 5804 5808 5810 5817 5818
[1285] 5826 5831 5833 5834 5835 5836 5843 5844 5847 5850 5854 5860
[1297] 5861 5865 5871 5872 5880 5881 5888 5890 5895 5903 5904 5906
[1309] 5920 5923 5924 5928 5934 5935 5936 5942 5946 5947 5949 5950
[1321] 5952 5953 5960 5961 5972 5979 5983 5986 5988 5989 5990 5992
[1333] 6009 6010 6020 6022 6025 6034 6035 6037 6044 6045 6046 6047
[1345] 6052 6053 6059 6060 6068 6069 6072 6081 6082 6083 6088 6094
[1357] 6105 6107 6108 6115 6119 6122 6130 6132 6136 6140 6159 6160
[1369] 6161 6170 6186 6188 6190 6195 6199 6214 6218 6223 6227 6228
[1381] 6231 6250 6252 6253 6259 6272 6274 6276 6285 6286 6287 6303
[1393] 6316 6319 6320 6323 6324 6329 6335 6340 6344 6347 6355 6359
[1405] 6363 6364 6370 6385 6397 6399 6401 6403 6406 6417 6423 6428
[1417] 6429 6437 6438 6446 6449 6451 6454 6460 6469 6474 6479 6482
[1429] 6490 6491 6496 6497 6498 6499 6506 6511 6515 6518 6526 6539
[1441] 6542 6544 6545 6550 6561 6577 6580 6582 6586 6589 6590 6600
[1453] 6604 6610 6611 6612 6621 6625 6626 6629 6634 6635 6644 6658
[1465] 6659 6662 6666 6670 6674 6677 6689 6690 6712 6718 6723 6726
[1477] 6727 6728 6732 6735 6738 6739 6742 6748 6749 6754 6756 6760
[1489] 6763 6765 6771 6787 6801 6804 6815 6816 6817 6820 6824 6829
[1501] 6830 6835 6847 6852 6856 6857 6858 6862 6864 6865 6871 6876
[1513] 6881 6886 6894 6895 6913 6918 6921 6925 6935 6941 6942 6944
[1525] 6947 6949 6953 6956 6960 6963 6964 6965 6974 6986 6992 6993
[1537] 6994 6996 6997 6999 7002 7004 7015 7018 7021 7025 7028 7029
[1549] 7030 7038 7056 7057 7058 7066 7071 7072 7077 7083 7101 7102
[1561] 7105 7107 7108 7109 7116 7133 7147 7153 7155 7160 7167 7173
[1573] 7176 7177 7181 7185 7200 7205 7209 7210 7218 7232 7235 7252
[1585] 7263 7266 7267 7272 7273 7276 7278 7279 7283 7292 7302 7307
[1597] 7309 7312 7315 7318 7319 7322 7326 7328 7331 7351 7354 7355
[1609] 7357 7361 7370 7371 7373 7374 7378 7382 7386 7392 7396 7401
[1621] 7402 7403 7416 7417 7424 7425 7428 7431 7439 7440 7441 7446
[1633] 7458 7459 7465 7470 7471 7482 7485 7491 7494 7498 7500 7504
[1645] 7510 7511 7514 7519 7520 7523 7532 7535 7536 7539 7546 7547
[1657] 7548 7550 7552 7565 7569 7577 7583 7588 7595 7599 7601 7602
[1669] 7607 7609 7611 7622 7623 7624 7626 7636 7637 7642 7645 7646
[1681] 7648 7662 7668 7669 7670 7671 7677 7679 7685 7686 7689 7692
[1693] 7693 7708 7709 7713 7721 7726 7728 7734 7736 7739 7748 7751
[1705] 7752 7755 7757 7767 7773 7785 7793 7796 7797 7800 7802 7805
[1717] 7806 7808 7812 7814 7818 7824 7828 7835 7837 7839 7851 7858
[1729] 7859 7862 7865 7866 7868 7869 7872 7875 7883 7886 7891 7894
[1741] 7898 7906 7911 7922 7928 7933 7942 7944 7948 7949 7950 7953
[1753] 7960 7961 7971 7972 7973 7990 7993 7994 7997 7999 8001 8005
[1765] 8008 8015 8016 8017 8021 8023 8025 8026 8027 8039 8044 8049
[1777] 8053 8058 8069 8070 8072 8080 8083 8088 8090 8093 8097 8108
[1789] 8123 8124 8137 8139 8140 8142 8144 8146 8151 8154 8157 8159
[1801] 8161 8170 8175 8178 8183 8192 8194 8208 8219 8228 8240 8241
[1813] 8245 8257 8262 8268 8272 8273 8274 8277 8293 8295 8296 8299
[1825] 8317 8319 8321 8325 8327 8329 8339 8342 8345 8347 8350 8351
[1837] 8352 8357 8358 8359 8363 8381 8387 8388 8394 8402 8406 8409
[1849] 8411 8415 8428 8445 8447 8451 8455 8461 8462 8464 8466 8467
[1861] 8469 8471 8479 8485 8490 8495 8499 8501 8502 8503 8505 8506
[1873] 8517 8523 8525 8527 8532 8533 8534 8540 8543 8546 8551 8552
[1885] 8561 8563 8568 8575 8589 8590 8595 8598 8607 8609 8612 8613
[1897] 8616 8623 8626 8631 8636 8637 8643 8645 8646 8649 8650 8654
[1909] 8656 8663 8664 8669 8674 8680 8686 8688 8690 8696 8697 8701
[1921] 8702 8706 8710 8713 8715 8719 8733 8736 8739 8740 8741 8744
[1933] 8745 8751 8753 8755 8778 8779 8784 8785 8788 8793 8801 8802
[1945] 8803 8806 8808 8811 8812 8815 8816 8817 8821 8827 8831 8836
[1957] 8842 8845 8846 8854 8861 8865 8867 8871 8872 8881 8883 8884
[1969] 8894 8897 8899 8900 8904 8905 8911 8912 8914 8915 8916 8927
[1981] 8931 8932 8933 8934 8943 8947 8948 8949 8950 8954 8955 8956
[1993] 8965 8968 8973 8974 8975 8977 8979 8980 8987 8988 8994 8999
[2005] 9007 9008 9009 9019 9021 9026 9036 9039 9046 9047 9048 9051
[2017] 9052 9053 9054 9056 9057 9068 9070 9072 9073 9074 9077 9078
[2029] 9079 9088 9089 9091 9094 9112 9113 9116 9117 9124 9125 9138
[2041] 9139 9143 9152 9154 9155 9157 9158 9159 9160 9166 9175 9177
[2053] 9178 9190 9195 9196 9197 9198 9199 9209 9210 9212 9213 9216
[2065] 9220 9221 9226 9228 9233 9240 9241 9244 9249 9251 9255 9258
[2077] 9261 9265 9273 9283 9286 9288 9298 9300 9309 9319 9330 9331
[2089] 9336 9342 9343 9344 9354 9361 9366 9368 9369 9376 9381 9387
[2101] 9388 9394 9395 9400 9405 9416 9420 9441 9449 9453 9468 9470
[2113] 9482 9486 9488 9491 9492 9495 9502 9507 9516 9526 9531 9533
[2125] 9541 9544 9545 9546 9551 9552 9553 9556 9557 9558 9561 9564
[2137] 9567 9569 9584 9586 9589 9590 9594 9608 9609 9610 9624 9632
[2149] 9637 9645 9648 9661 9666 9667 9671 9679 9680 9682 9684 9690
[2161] 9691 9695 9696 9698 9703 9704 9713 9715 9716 9717 9719 9721
[2173] 9726 9730 9734 9735 9737 9738 9743 9751 9757 9758 9761 9772
[2185] 9773 9778 9789 9792 9797 9800 9801 9808 9817 9821 9823 9831
[2197] 9838 9839 9850 9853 9857 9867 9878 9882 9889 9895 9901 9904
[2209] 9909 9925 9926 9931 9939 9943 9946 9949 9952 9956 9957 9960
[2221] 9966 9968 9969 9971 9973 9981 9991 9992 10004 10006 10008 10015
[2233] 10024 10025 10026 10030 10033 10037 10040 10048 10052 10077 10080 10081
[2245] 10104 10107 10109 10111 10121 10125 10142 10143 10148 10151 10153 10154
[2257] 10162 10170 10174 10175 10179 10187 10197 10206 10210 10211 10212 10215
[2269] 10223 10224 10225 10230 10240 10241 10245 10250 10251 10253 10255 10256
[2281] 10257 10261 10262 10264 10265 10269 10276 10283 10284 10286 10295 10299
[2293] 10300 10306 10318 10324 10333 10334 10347 10350 10351 10353 10386 10390
[2305] 10394 10398 10401 10415 10416 10423 10424 10426 10429 10431 10437 10439
[2317] 10442 10450 10458 10466 10470 10474 10475 10476 10477 10481 10482 10490
[2329] 10494 10499 10501 10506 10508 10509 10513 10517 10518 10519 10521 10524
[2341] 10537 10541 10550 10567 10568 10581 10589 10600 10601 10603 10609 10632
[2353] 10634 10636 10660 10663 10670 10675 10677 10679 10681 10682 10684 10689
[2365] 10691 10692 10695 10697 10701 10702 10703 10707 10708 10719 10720 10721
[2377] 10722 10729 10732 10733 10737 10740 10743 10744 10745 10748 10757 10762
[2389] 10763 10770 10781 10783 10788 10797 10798 10799 10801 10802 10803 10804
[2401] 10806 10812 10813 10814 10816 10819 10836 10842 10846 10852 10863 10866
[2413] 10869 10873 10874 10877 10878 10880 10891 10901 10912 10913 10916 10920
[2425] 10923 10928 10929 10931 10934 10936 10937 10939 10945 10948 10954 10956
[2437] 10958 10961 10962 10964 10966 10968 10971 10975 10976 10978 10981 10986
[2449] 10987 10993 10994 10995 11001 11005 11006 11007 11009 11011 11014 11018
[2461] 11022 11026 11028 11032 11033 11040 11044 11050 11056 11058 11059 11066
[2473] 11075 11076 11077 11083 11085 11088 11089 11099 11103 11104 11117 11119
[2485] 11120 11121 11122 11123 11131 11134 11137 11138 11142 11143 11144 11147
[2497] 11176 11177 11179 11184 11185 11194 11196 11198 11202 11208 11212 11213
[2509] 11214 11215 11218 11223 11229 11233 11235 11241 11243 11249 11256 11258
[2521] 11260 11262 11267 11278 11291 11307 11312 11316 11317 11318 11319 11321
[2533] 11327 11328 11331 11332 11333 11335 11337 11340 11343 11354 11356 11358
[2545] 11359 11360 11362 11366 11367 11382 11388 11392 11393 11394 11397 11398
[2557] 11399 11404 11406 11409 11413 11415 11424 11425 11429 11432 11435 11436
[2569] 11438 11439 11440 11445 11448 11450 11453 11455 11458 11463 11468 11470
[2581] 11478 11480 11482 11483 11489 11490 11497 11499 11510 11513 11518 11519
[2593] 11529 11530 11531 11534 11536 11544 11545 11546 11555 11567 11569 11571
[2605] 11572 11573 11575 11576 11579 11583 11584 11593 11601 11603 11605 11612
[2617] 11615 11620 11640 11643 11649 11656 11664 11670 11675 11681 11690 11691
[2629] 11692 11696 11716 11719 11723 11724 11728 11732 11736 11740 11741 11743
[2641] 11746 11747 11748 11754 11760 11762 11766 11768 11769 11771 11773 11778
[2653] 11782 11789 11797 11801 11804 11805 11807 11808 11809 11813 11817 11820
[2665] 11834 11835 11836 11845 11847 11855 11859 11864 11866 11879 11886 11895
[2677] 11897 11898 11900 11903 11913 11917 11922 11923 11924 11925 11926 11929
[2689] 11931 11939 11942 11944 11950 11951 11962 11972 11973 11974 11975 11976
[2701] 11980 11981 11982 11983 11987 11988 11989 11996 12001 12003 12011 12012
[2713] 12026 12031 12037 12041 12047 12056 12061 12065 12071 12078 12090 12091
[2725] 12094 12098 12099 12100 12111 12119 12124 12128 12140 12141 12149 12150
[2737] 12151 12153 12158 12168 12173 12176 12178 12179 12180 12181 12184 12185
[2749] 12187 12190 12193 12199 12201 12203 12209 12212 12213 12229 12230 12233
[2761] 12238 12247 12248 12249 12256 12264 12265 12267 12274 12275 12276 12283
[2773] 12290 12291 12296 12300 12301 12320 12326 12334 12335 12345 12347 12357
[2785] 12360 12361 12364 12370 12371 12372 12377 12382 12386 12395 12396 12400
[2797] 12401 12404 12408 12410 12418 12426 12427 12430 12442 12443 12446 12449
[2809] 12450 12451 12452 12456 12457 12460 12463 12479 12480 12482 12496 12502
[2821] 12513 12520 12540 12545 12549 12564 12567 12584 12587 12588 12596 12597
[2833] 12600 12604 12629 12633 12634 12635 12641 12646 12653 12655 12656 12658
[2845] 12659 12660 12676 12681 12682 12688 12693 12700 12701 12707 12727 12731
[2857] 12741 12745 12747 12751 12755 12764 12766 12782 12783 12785 12790 12794
[2869] 12806 12807 12812 12813 12815 12816 12818 12839 12842 12845 12847 12850
[2881] 12856 12857 12858 12862 12864 12865 12867 12875 12880 12887 12894 12912
[2893] 12916 12924 12931 12939 12945 12961 12964 12965 12967 12968 12969 12972
[2905] 12973 12975 12988 12991 13001 13003 13005 13007 13010 13014 13019 13020
[2917] 13023 13036 13037 13049 13055 13057 13061 13065 13066 13071 13075 13076
[2929] 13079 13092 13105 13107 13108 13117 13125 13129 13130 13132 13135 13142
[2941] 13144 13147 13156 13157 13158 13160 13166 13168 13181 13182 13183 13191
[2953] 13193 13196 13200 13201 13202 13205 13209 13212 13216 13218 13223 13242
[2965] 13246 13247 13250 13270 13273 13274 13278 13287 13292 13294 13297 13299
[2977] 13307 13310 13311 13321 13323 13325 13331 13334 13339 13344 13348 13349
[2989] 13351 13352 13353 13355 13359 13360 13369 13372 13373 13378 13381 13382
[3001] 13388 13392 13400 13403 13407 13413 13415 13416 13423 13425 13429 13431
[3013] 13432 13433 13436 13441 13442 13443 13448 13449 13465 13466 13470 13471
[3025] 13479 13496 13498 13499 13500 13502 13510 13513 13522 13526 13530 13534
[3037] 13546 13551 13558 13561 13563 13564 13569 13573 13574 13576 13581 13585
[3049] 13586 13598 13606 13617 13623 13627 13629 13632 13633 13641 13647 13649
[3061] 13650 13652 13656 13657 13661 13676 13677 13680 13688 13689 13690 13694
[3073] 13695 13699 13700 13704 13709 13710 13719 13720 13728 13729 13730 13731
[3085] 13736 13740 13752 13753 13754 13763 13764 13770 13785 13788 13796 13800
[3097] 13801 13803 13809 13813 13816 13823 13824 13832 13833 13834 13836 13838
[3109] 13842 13845 13846 13847 13848 13857 13865 13869 13870 13876 13878 13881
[3121] 13893 13897 13904 13914 13915 13918 13922 13932 13934 13937 13941 13947
[3133] 13960 13962 13967 13969 13970 13973 13974 13976 13978 13981 13982 13989
[3145] 13992 13999 14001 14002 14013 14016 14017 14019 14025 14030 14032 14042
[3157] 14044 14045 14052 14060 14064 14069 14078 14080 14081 14082 14083 14086
[3169] 14094 14100 14102 14107 14109 14117 14120 14125 14127 14131 14132 14134
[3181] 14137 14140 14141 14143 14144 14156 14157 14161 14163 14170 14176 14177
[3193] 14182 14186 14187 14192 14194 14197 14198 14204 14206 14210 14214 14216
[3205] 14218 14219 14220 14225 14226 14236 14238 14239 14244 14247 14264 14268
[3217] 14272 14274 14278 14279 14280 14287 14292 14309 14311 14318 14328 14330
[3229] 14331 14335 14336 14337 14354 14367 14369 14372 14378 14382 14385 14387
[3241] 14392 14393 14394 14399 14400 14404 14413 14419 14420 14422 14430 14436
[3253] 14445 14447 14450 14461 14464 14465 14473 14476 14481 14486 14493 14496
[3265] 14497 14499 14501 14505 14509 14512 14514 14519 14524 14525 14526 14528
[3277] 14529 14531 14533 14542 14544 14548 14549 14552 14556 14559 14570 14580
[3289] 14583 14587 14589 14591 14610 14613 14623 14625 14639 14646 14665 14668
[3301] 14672 14673 14674 14675 14678 14683 14685 14686 14689 14692 14698 14699
[3313] 14701 14705 14706 14718 14727 14731 14735 14736 14738 14740 14742 14744
[3325] 14745 14756 14761 14770 14773 14783 14787 14788 14791 14800 14801 14809
[3337] 14812 14815 14816 14823 14837 14842 14848 14853 14857 14860 14865 14866
[3349] 14867 14871 14879 14880 14882 14896 14900 14903 14924 14926 14928 14929
[3361] 14933 14936 14947 14954 14958 14959 14963 14976 14990 14992 14993 15000
[3373] 15007 15009 15010 15013 15026 15028 15030 15032 15038 15042 15050 15055
[3385] 15063 15067 15070 15072 15079 15081 15092 15093 15096 15100 15114 15115
[3397] 15116 15121 15126 15137 15141 15143 15151 15152 15159 15160 15163 15171
[3409] 15174 15176 15177 15184 15189 15191 15195 15202 15203 15205 15206 15210
[3421] 15213 15221 15229 15232 15233 15239 15240 15256 15262 15263 15265 15269
[3433] 15278 15282 15295 15311 15314 15315 15318 15322 15324 15326 15328 15332
[3445] 15335 15337 15345 15347 15348 15351 15363 15365 15369 15370 15386 15388
[3457] 15397 15408 15410 15419 15423 15427 15432 15436 15437 15452 15456 15463
[3469] 15467 15469 15475 15478 15487 15490 15491 15496 15505 15512 15513 15519
[3481] 15523 15526 15527 15530 15532 15535 15536 15544 15546 15547 15549 15554
[3493] 15560 15564 15565 15569 15570 15571 15572 15574 15576 15577 15584 15590
[3505] 15591 15596 15599 15600 15617 15619 15621 15622 15625 15632 15635 15643
[3517] 15648 15650 15651 15659 15660 15674 15676 15679 15693 15700 15701 15702
[3529] 15703 15707 15713 15727 15729 15739 15741 15748 15753 15758 15759 15761
[3541] 15762 15768 15769 15772 15774 15779 15784 15785 15788 15794 15798 15802
[3553] 15803 15806 15811 15812 15825 15826 15830 15835 15838 15840 15842 15843
[3565] 15846 15851 15852 15855 15860 15863 15879 15887 15892 15893 15906 15908
[3577] 15910 15911 15922 15933 15934 15935 15938 15939 15940 15943 15958 15959
[3589] 15963 15967 15968 15977 15980 15981 15984 15990 16006 16008 16021 16023
[3601] 16024 16029 16031 16034 16036 16037 16043 16045 16049 16053 16057 16058
[3613] 16060 16068 16070 16071 16076 16078 16081 16088 16094 16105 16115 16122
[3625] 16125 16126 16128 16130 16132 16133 16134 16135 16137 16140 16143 16145
[3637] 16146 16150 16158 16169 16172 16178 16181 16192 16199 16207 16211 16212
[3649] 16213 16218 16226 16235 16238 16239 16251 16253 16264 16274 16276 16278
[3661] 16287 16292 16295 16302 16308 16309 16311 16314 16315 16324 16328 16329
[3673] 16330 16331 16334 16338 16340 16341 16349 16350 16355 16359 16362 16363
[3685] 16366 16368 16369 16370 16386 16387 16388 16391 16392 16405 16414 16426
[3697] 16431 16438 16440 16441 16447 16451 16455 16457 16459 16460 16478 16480
[3709] 16485 16486 16490 16493 16501 16503 16506 16507 16509 16510 16516 16519
[3721] 16522 16526 16527 16528 16543 16546 16548 16551 16553 16554 16555 16557
[3733] 16560 16562 16563 16570 16571 16583 16586 16589 16591 16595 16602 16604
[3745] 16613 16617 16631 16633 16636 16637 16641 16649 16650 16652 16653 16656
[3757] 16660 16667 16674 16677 16681 16688 16694 16695 16699 16700 16701 16704
[3769] 16709 16714 16722 16723 16724 16731 16732 16739 16744 16752 16753 16762
[3781] 16765 16770 16772 16783 16784 16787 16789 16793 16795 16797 16806 16807
[3793] 16809 16813 16814 16815 16816 16821 16830 16832 16835 16838 16840 16841
[3805] 16848 16859 16869 16873 16885 16886 16893 16898 16902 16904 16907 16909
[3817] 16919 16921 16928 16934 16936 16946 16948 16967 16971 16973 16975 16976
[3829] 16980 16987 16995 16996 17000 17004 17009 17014 17019 17020 17021 17025
[3841] 17030 17031 17032 17037 17052 17055 17057 17059 17064 17067 17083 17094
[3853] 17098 17103 17106 17121 17123 17129 17140 17145 17146 17148 17149 17156
[3865] 17159 17160 17164 17165 17169 17170 17172 17174 17177 17182 17184 17189
[3877] 17191 17193 17194 17200 17201 17210 17219 17220 17226 17229 17233 17239
[3889] 17252 17258 17270 17280 17283 17293 17296 17306 17309 17311 17312 17324
[3901] 17325 17331 17341 17342 17352 17353 17356 17359 17363 17367 17370 17375
[3913] 17376 17377 17378 17379 17381 17390 17394 17401 17412 17415 17416 17421
[3925] 17423 17440 17445 17447 17448 17452 17462 17464 17466 17473 17478 17487
[3937] 17493 17496 17498 17499 17501 17504 17506 17515 17516 17518 17524 17526
[3949] 17528 17530 17535 17541 17542 17543 17545 17547 17548 17549 17554 17559
[3961] 17560 17570 17572 17575 17576 17579 17582 17586 17591 17597 17613 17614
[3973] 17616 17617 17618 17619 17620 17623 17625 17628 17635 17645 17650 17652
[3985] 17653 17662 17665 17666 17667 17668 17671 17674 17676 17680 17683 17685
[3997] 17692 17693 17695 17696 17701 17702 17708 17712 17714 17719 17725 17729
[4009] 17744 17754 17755 17756 17758 17761 17771 17772 17780 17783 17790 17792
[4021] 17793 17805 17806 17811 17823 17824 17825 17827 17838 17839 17842 17852
[4033] 17856 17869 17871 17877 17879 17881 17888 17899 17917 17924 17926 17932
[4045] 17934 17938 17939 17947 17950 17953 17955 17956 17957 17968 17969 17972# combine the indexed loci with loci names
index_178names <- locNames(vac.pops)[index_178]
# make a new genlight object with only those indexed loci
vac.gl_178 <- gl.keep.loc(vac.pops, loc.list = index_178names)Starting gl.keep.loc
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
List of loci to keep has been specified
Deleting all but the specified loci
Completed: gl.keep.loc vac.gl_178 <- gl.compliance.check(vac.gl_178)Starting gl.compliance.check
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Checking coding of SNPs
SNP data scored NA, 0, 1 or 2 confirmed
Checking for population assignments
Population assignments confirmed
Checking locus metrics and flags
Recalculating locus metrics
Checking for monomorphic loci
Dataset contains monomorphic loci
Checking for loci with all missing data
Dataset contains loci with all missing dat
Checking whether individual names are unique.
Checking for individual metrics
Individual metrics confirmed
Spelling of coordinates checked and changed if necessary to
lat/lon
Completed: gl.compliance.check vac.gl_178 ********************
*** DARTR OBJECT ***
********************
** 34 genotypes, 4,056 SNPs , size: 91.2 Mb
missing data: 27488 (=19.93 %) scored as NA
** Genetic data
@gen: list of 34 SNPbin
@ploidy: ploidy of each individual (range: 2-2)
** Additional data
@ind.names: 34 individual labels
@loc.names: 4056 locus labels
@loc.all: 4056 allele labels
@position: integer storing positions of the SNPs [within 69 base sequence]
@pop: population of each individual (group size range: 5-22)
@other: a list containing: loc.metrics, ind.metrics, latlon, loc.metrics.flags, history, verbose
@other$ind.metrics: id, species, ind, pop, sex, lat, lon, e, n, karyo, PCR1, DAPI, FISH
@other$loc.metrics: AlleleID, CloneID, AlleleSequence, TrimmedSequence, Chrom_Komodo_dragon_NCBIv1, ChromPos_Komodo_dragon_NCBIv1, AlnCnt_Komodo_dragon_NCBIv1, AlnEvalue_Komodo_dragon_NCBIv1, Chrom_Varanus_JD_infer_z, ChromPos_Varanus_JD_infer_z, AlnCnt_Varanus_JD_infer_z, AlnEvalue_Varanus_JD_infer_z, Chrom_Varanus_JD_vac_aligned_chr6_7, ChromPos_Varanus_JD_vac_aligned_chr6_7, AlnCnt_Varanus_JD_vac_aligned_chr6_7, AlnEvalue_Varanus_JD_vac_aligned_chr6_7, Chrom_Varanus_JD_infer_w, ChromPos_Varanus_JD_infer_w, AlnCnt_Varanus_JD_infer_w, AlnEvalue_Varanus_JD_infer_w, SNP, SnpPosition, CallRate, OneRatioRef, OneRatioSnp, FreqHomRef, FreqHomSnp, FreqHets, PICRef, PICSnp, AvgPIC, AvgCountRef, AvgCountSnp, RepAvg, clone, uid, rdepth, maf, monomorphs, OneRatio, PIC
@other$latlon[g]: coordinates for all individuals are attachedvac.gl_178 <- gl.keep.pop(vac.gl_178, c("AA", "MA", "MM"))Starting gl.keep.pop
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Checking for presence of nominated populations
Retaining only populations AA, MA, MM
Warning: Resultant dataset may contain monomorphic loci
Locus metrics not recalculated
Completed: gl.keep.pop table(vac.gl_178$pop)
AA MA MM
5 7 22 # Concantenate the SNPs for scaf_178 for phylogenetic inference-----------------
# The .FASTA file was used as input sequences for Genieous Prime
fasta <-
gl2fasta(
vac.gl_178,
method = 3,
outfile = "./data/vac.gl_178_concat.fasta",
outpath = getwd(),
verbose = 3
)Starting gl2fasta
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Warning: Dataset contains monomorphic loci which will be included in the output fasta file
Assigning ambiguity codes to heterozygote SNPs, concatenating SNPs
Removing loci for which SNP position is outside the length of the trimmed sequences
Generating haplotypes ... This may take some time
Completed: gl2fasta # Supplementary Figure 4--------------------------------------------------------
vac.pops_temp <- gl.filter.callrate(vac.gl_178, threshold = 1)Starting gl.filter.callrate
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Warning: Data may include monomorphic loci in call rate
calculations for filtering
Recalculating Call Rate
Removing loci based on Call Rate, threshold = 1 
Completed: gl.filter.callrate gl.smearplot(
vac.pops_temp,
ind.labels = T,
plot.colors = c('royalblue',
'yellow', 'red'),
label.size = 6,
group.pop = T
) Processing genlight object with SNP data
Starting gl.smearplot 
Completed: gl.smearplot vac.pops_temp ********************
*** DARTR OBJECT ***
********************
** 34 genotypes, 874 SNPs , size: 89.8 Mb
missing data: 0 (=0 %) scored as NA
** Genetic data
@gen: list of 34 SNPbin
@ploidy: ploidy of each individual (range: 2-2)
** Additional data
@ind.names: 34 individual labels
@loc.names: 874 locus labels
@loc.all: 874 allele labels
@position: integer storing positions of the SNPs [within 69 base sequence]
@pop: population of each individual (group size range: 5-22)
@other: a list containing: loc.metrics, ind.metrics, latlon, loc.metrics.flags, history, verbose
@other$ind.metrics: id, species, ind, pop, sex, lat, lon, e, n, karyo, PCR1, DAPI, FISH
@other$loc.metrics: AlleleID, CloneID, AlleleSequence, TrimmedSequence, Chrom_Komodo_dragon_NCBIv1, ChromPos_Komodo_dragon_NCBIv1, AlnCnt_Komodo_dragon_NCBIv1, AlnEvalue_Komodo_dragon_NCBIv1, Chrom_Varanus_JD_infer_z, ChromPos_Varanus_JD_infer_z, AlnCnt_Varanus_JD_infer_z, AlnEvalue_Varanus_JD_infer_z, Chrom_Varanus_JD_vac_aligned_chr6_7, ChromPos_Varanus_JD_vac_aligned_chr6_7, AlnCnt_Varanus_JD_vac_aligned_chr6_7, AlnEvalue_Varanus_JD_vac_aligned_chr6_7, Chrom_Varanus_JD_infer_w, ChromPos_Varanus_JD_infer_w, AlnCnt_Varanus_JD_infer_w, AlnEvalue_Varanus_JD_infer_w, SNP, SnpPosition, CallRate, OneRatioRef, OneRatioSnp, FreqHomRef, FreqHomSnp, FreqHets, PICRef, PICSnp, AvgPIC, AvgCountRef, AvgCountSnp, RepAvg, clone, uid, rdepth, maf, monomorphs, OneRatio, PIC
@other$latlon[g]: coordinates for all individuals are attachedFurther Study
Link to github repository of GENESPACE: https://github.com/jtlovell/GENESPACE/tree/master
Dobry, Zhu, et al. (2023)
Dobry, Wapstra, et al. (2023)