Post date: Jun 08, 2014 6:41:25 PM
I made a few figures and a table to summarize the single locus LMM gemma analyses. This includes Manhattan plots of P-values from Wald's test with genome-wide significance designated as 0.05/(no. loci), and a table of the null PVE, number of significant SNPs, and PVE for those significant SNPs. I calculated the latter in R from a linear model after removing any relevant covariates.
Here are the scaffold and positions number for significant SNPs (not scaffold 29 shows up twice for survival-all, and sc110pos113 shows up for survival-all and survival-Sla with the same sign).
survival, all
"sc29pos42281" "sc29pos42294" "sc110pos113" "sc3562pos17314" "sc10793pos4346"
survival, Sla
"sc110pos113"
survival, Gla
"sc36pos248085"
survival, SLA x Ac
"sc29pos164306" "sc45pos178842" "sc51pos151626" "sc93pos13457" "sc132pos233998" "sc140pos12388" "sc179pos11199" "sc204pos70313" "sc209pos147351" "sc325pos136450" "sc383pos78394" "sc395pos103045" "sc401pos140407" "sc467pos76262" "sc467pos76263" "sc539pos30701" "sc689pos73917" "sc695pos46583" "sc700pos9378" "sc733pos898" "sc981pos29142" "sc1085pos49247" "sc1230pos55568" "sc1315pos58697" "sc1625pos8158" "sc1641pos4947" "sc1661pos31413" "sc1876pos49320" "sc2347pos28261" "sc2376pos27843" "sc2554pos24683" "sc2732pos21146" "sc3763pos14076" "sc4583pos10566" "sc4842pos5525" "sc6964pos15748" "sc8269pos6710" "sc11858pos3260"
weight, Gla x Ms
"sc1574pos23726"
wegith, Ac
"sc7pos147334"