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 mr1247 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
vg1008520987 sf1008449849 10 8520987 2.83E-17 1.19E-10
vg1007942238 sf1007957848 10 7942238 6.91E-15 8.49E-10
vg1005818268 sf1005834806 10 5818268 1.79E-14 2.44E-08
vg1204314449 sf1204313437 12 4314449 4.62E-14 7.87E-09
vg0407824132 sf0407819400 4 7824132 6.72E-14 4.72E-07
vg1005800261 sf1005816799 10 5800261 2.08E-13 2.15E-08
vg0905249361 sf0905248361 9 5249361 3.26E-13 NA
vg1216843085 sf1216837039 12 16843085 4.43E-13 4.80E-08
vg0403205910 sf0403201513 4 3205910 7.00E-11 1.51E-08
vg0813089324 sf0813086954 8 13089324 7.02E-11 7.12E-07
vg0502009146 sf0502009128 5 2009146 2.29E-09 4.58E-08
vg1006376447 sf1006392070 10 6376447 2.51E-08 5.04E-07
vg0504390095 sf0504390072 5 4390095 1.36E-07 3.92E-07
vg1010606791 sf1010535612 10 10606791 3.56E-07 1.31E-06
vg0501612224 sf0501612208 5 1612224 4.01E-07 1.43E-06
vg0222725905 sf0222720036 2 22725905 4.29E-07 3.37E-11
vg0224748988 sf0224743119 2 24748988 1.71E-06 3.81E-07
vg0222724011 sf0222718142 2 22724011 2.39E-06 4.63E-10
vg0110637699 sf0110636675 1 10637699 5.12E-06 NA
vg0222581124 sf0222575255 2 22581124 7.62E-06 6.53E-08
vg0912675777 sf0912674776 9 12675777 7.89E-06 6.89E-07
vg0225036530 sf0225030661 2 25036530 NA 8.77E-08
vg0526696589 sf0526633947 5 26696589 NA 4.03E-07
vg1111385027 sf1111379344 11 11385027 NA 5.77E-07
vg0417689977 sf0417518018 4 17689977 NA 6.90E-07
vg0222726952 sf0222721083 2 22726952 NA 3.98E-06