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 mr1120 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 2.12E-18 1.71E-11
vg1005905764 sf1005922302 10 5905764 2.14E-15 7.45E-09
vg1204314449 sf1204313437 12 4314449 5.98E-15 8.16E-09
vg1005800261 sf1005816799 10 5800261 6.10E-15 3.36E-09
vg0407825479 sf0407820747 4 7825479 1.43E-14 2.82E-07
vg1216843085 sf1216837039 12 16843085 1.77E-14 1.02E-08
vg0403205910 sf0403201513 4 3205910 1.98E-13 3.43E-09
vg0403205033 sf0403200636 4 3205033 5.61E-13 3.75E-06
vg1006959353 sf1006974976 10 6959353 6.39E-12 1.01E-07
vg0813089324 sf0813086954 8 13089324 8.62E-11 2.79E-06
vg1007452452 sf1007468075 10 7452452 3.91E-10 7.74E-07
vg0502009146 sf0502009128 5 2009146 4.52E-09 5.82E-07
vg1010606791 sf1010535612 10 10606791 5.77E-08 3.63E-06
vg0503608486 sf0503608463 5 3608486 1.50E-07 2.12E-06
vg0308122080 sf0308121018 3 8122080 3.64E-07 NA
vg0224748988 sf0224743119 2 24748988 4.63E-07 1.12E-07
vg0204625031 sf0204625028 2 4625031 1.91E-06 4.32E-06
vg1118246821 sf1117780680 11 18246821 3.43E-06 NA
vg0332229293 sf0332222171 3 32229293 6.23E-06 NA
vg0222725905 sf0222720036 2 22725905 NA 1.34E-08
vg0335766999 sf0335759868 3 35766999 NA 1.94E-06
vg1111385027 sf1111379344 11 11385027 NA 1.98E-06
vg0222271516 sf0222265647 2 22271516 NA 1.99E-06
vg0525094756 sf0525032171 5 25094756 NA 2.65E-06
vg0624862159 sf0624861162 6 24862159 NA 4.38E-06
vg1113477515 sf1113013837 11 13477515 NA 8.51E-06