Post date: Jun 13, 2014 4:44:29 PM
I grabbed the the details on the repetitive elements that were enriched for SNP associations. These are summarized below (each row begins with the scaffold and position of the SNP), and some useful R code is at the end. Trait-associated SNV's that were enriched for repeats included 21 transposable element associations (75%) and 7 low-complexity repeat associations (25%). These are not all unique elements.
Wgt, GLA x Ac
11 363496 name=species:BEL-630_AA-I|genus:LTR%2FPao;Target=species:BEL-630_AA-I|genus:LTR%2FPao (my note, this is an BEL-Pao LTR retrotransposon)
963 47974 ZENON_BM|genus:LINE%2FCR1;Target=species:ZENON_BM|genus:LINE%2FCR1
963 48112 ZENON_BM|genus:LINE%2FCR1;Target=species:ZENON_BM|genus:LINE%2FCR1
1135 30083 Name=species:Helitron-N2_DBp|genus:RC%2FHelitron;Target=species:Helitron-N2_DBp|genus:RC%2FHelitron (my note, helitorns are transposons)
Wgt, SLA x Ms
326 1504 Name=species:A-rich|genus:Low_complexity;Target=species:A-rich|genus:Low_complexity
8603 1756 Name=species:Mariner-1_BM|genus:DNA%2FTcMar-Mariner;Target=species:Mariner-1_BM|genus:DNA%2FTcMar-Mariner (my note, this is a tranposable element)
Survival, Ac
104 118181 Name=species:A-rich|genus:Low_complexity;Target=species:A-rich|genus:Low_complexity
3989 17148 Name=species:%28GCGCCG%29n|genus:Simple_repeat;Target=species:%28GCGCCG%29n|genus:Simple_repeat
3989 17153 Name=species:%28GCGCCG%29n|genus:Simple_repeat;Target=species:%28GCGCCG%29n|genus:Simple_repeat
6065 126 Name=species:Jockey-1_DWi|genus:LINE%2FJockey;Target=species:Jockey-1_DWi|genus:LINE%2FJockey
8203 128 Name=species:ZENON_BM|genus:LINE%2FCR1;Target=species:ZENON_BM|genus:LINE%2FCR1 (my note, this transposable element shows up again above)
Survival, all
201 57587 Name=species:A-rich|genus:Low_complexity;Target=species:A-rich|genus:Low_complexity
624 54873 Name=species:Helitron-N2_DBp|genus:RC%2FHelitron;Target=species:Helitron-N2_DBp|genus:RC%2FHelitron (we have seen this one above too)
6065 126 Name=species:Jockey-1_DWi|genus:LINE%2FJockey;Target=species:Jockey-1_DWi|genus:LINE%2FJockey (also in survival, Ac)
7608 5550 Name=species:Gypsy-7_HMM-I|genus:LTR%2FGypsy;Target=species:Gypsy-7_HMM-I|genus:LTR%2FGypsy
Survival, SLA
201 57587 Name=species:A-rich|genus:Low_complexity;Target=species:A-rich|genus:Low_complexity
338 146615 Name=species:ZENON_BM|genus:LINE%2FCR1;Target=species:ZENON_BM|genus:LINE%2FCR1
857 51454 Name=species:%28AGGAC%29n|genus:Simple_repeat;Target=species:%28AGGAC%29n|genus:Simple_repeat
963 48091 ZENON_BM|genus:LINE%2FCR1;Target=species:ZENON_BM|genus:LINE%2FCR1 (my note, seen this exact region before: wgt GLA x Ac)
7608 5550 Name=species:Gypsy-7_HMM-I|genus:LTR%2FGypsy;Target=species:Gypsy-7_HMM-I|genus:LTR%2FGypsy
Wgt, Ms
660 67591 Name=species:Loa-1_DEl|genus:LINE%2FLOA;Target=species:Loa-1_DEl|genus:LINE%2FLOA
722 24059 Name=species:Lep1|genus:SINE?;Target=species:Lep1|genus:SINE?
2092 7073 Name=species:DIRS_Nvi|genus:LTR%2FDIRS;Target=species:DIRS_Nvi|genus:LTR%2FDIRS (my note, this is also a type of transposable element)
12113 29 Name=species:ZENON_BM|genus:LINE%2FCR1;Target=species:ZENON_BM|genus:LINE%2FCR1
Wgt, SLA
3991 22686 Name=species:CR1-7_NVi|genus:LINE%2FL2;Target=species:CR1-7_NVi|genus:LINE%2FL2
12113 29 Name=species:ZENON_BM|genus:LINE%2FCR1;Target=species:ZENON_BM|genus:LINE%2FCR1
Wgt, all
3991 22686 Name=species:CR1-7_NVi|genus:LINE%2FL2;Target=species:CR1-7_NVi|genus:LINE%2FL2
12113 29 Name=species:ZENON_BM|genus:LINE%2FCR1;Target=species:ZENON_BM|genus:LINE%2FCR1
R code used for this (with annotTests.rwsp)
j<-2
trt<-j+2
obs<-abs(wgtC[which(is.na(wgtC[,trt])==FALSE),c(1:2,trt)])
bnd<-quantile(obs[,3],probs=0.9995)
top<-which(obs[,3] > bnd)
X<-XwgtComb
obs.rep<-annot$onrep[X[[j]]]
scaf<-annot$scaf[X[[j]]]
pos<-annot$pos[X[[j]]]
cbind(scaf[top],pos[top],obs.rep[top])