Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1108 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0610566343 sf0610565344 6 10566343 7.89E-117 3.84E-40
vg0610435427 sf0610434428 6 10435427 6.46E-110 1.44E-34
vg0616950705 sf0616949708 6 16950705 1.34E-70 NA
vg0610832091 sf0610831092 6 10832091 3.37E-68 3.76E-10
vg0719259692 sf0719258699 7 19259692 3.14E-66 NA
vg0627250403 sf0627249406 6 27250403 8.03E-65 NA
vg0304920678 sf0304919680 3 4920678 1.01E-64 NA
vg0610763769 sf0610762770 6 10763769 NA 3.32E-15
vg0610444069 sf0610443070 6 10444069 NA 1.15E-12
vg0610813890 sf0610812891 6 10813890 NA 3.20E-11
vg0610702326 sf0610701327 6 10702326 NA 3.43E-10
vg0609929059 sf0609928060 6 9929059 NA 3.89E-10
vg0611682950 sf0611681951 6 11682950 NA 4.12E-10
vg0610487099 sf0610486100 6 10487099 NA 6.00E-10
vg0610069455 sf0610068456 6 10069455 NA 5.18E-09
vg0609903452 sf0609902453 6 9903452 NA 8.01E-09
vg0613067756 sf0613066757 6 13067756 NA 5.93E-08
vg0617623926 sf0617622929 6 17623926 NA 7.06E-08
vg0610393322 sf0610392323 6 10393322 NA 1.12E-07
vg0614785443 sf0614784444 6 14785443 NA 1.64E-07
vg0611636429 sf0611635430 6 11636429 NA 2.19E-07
vg0610929434 sf0610928435 6 10929434 NA 3.16E-07
vg0610026311 sf0610025312 6 10026311 NA 3.27E-07
vg0611125709 sf0611124710 6 11125709 NA 5.00E-07
vg0518201525 sf0518141011 5 18201525 NA 5.93E-07
vg0515926609 sf0515869116 5 15926609 NA 7.05E-07