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 mr1047 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
vg0917982727 sf0917981726 9 17982727 7.15E-08 8.01E-07
vg0904628790 sf0904627790 9 4628790 1.40E-07 4.89E-06
vg1000569106 sf1000568082 10 569106 9.42E-07 3.78E-06
vg0100044434 sf0100043434 1 44434 1.90E-06 9.92E-06
vg1226996981 sf1226963380 12 26996981 2.23E-06 3.48E-07
vg0336295511 sf0336288381 3 36295511 2.65E-06 1.72E-06
vg0918217541 sf0918216540 9 18217541 2.67E-06 3.95E-06
vg0406946959 sf0406942227 4 6946959 9.14E-06 4.31E-06
vg0114152314 sf0114151288 1 14152314 NA 1.30E-06
vg0620733763 sf0620732766 6 20733763 NA 1.65E-06
vg0139380327 sf0139379284 1 39380327 NA 2.14E-06
vg0822230939 sf0822228226 8 22230939 NA 3.21E-06