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 mr1194 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
vg0232347492 sf0232341623 2 32347492 1.48E-60 NA
vg0135952423 sf0135951380 1 35952423 3.14E-60 5.60E-06
vg0822066769 sf0822064056 8 22066769 1.68E-59 NA
vg0900659002 sf0900658002 9 659002 1.82E-58 NA
vg0805970832 sf0805969835 8 5970832 2.17E-58 NA
vg0822296656 sf0822293943 8 22296656 2.04E-54 2.21E-06
vg0805771768 sf0805770771 8 5771768 2.15E-53 1.58E-06
vg0100543265 sf0100542265 1 543265 NA 5.31E-09
vg0217639783 sf0217633913 2 17639783 NA 4.32E-08
vg0133432014 sf0133430970 1 33432014 NA 6.90E-08
vg0525944770 sf0525882191 5 25944770 NA 2.25E-07
vg0906746271 sf0906745271 9 6746271 NA 6.51E-07
vg1011651673 sf1011580488 10 11651673 NA 8.28E-07
vg0526991032 sf0526928388 5 26991032 NA 3.37E-06
vg0422506796 sf0422321683 4 22506796 NA 3.53E-06
vg0826412433 sf0826409719 8 26412433 NA 3.57E-06
vg1124662697 sf1124196537 11 24662697 NA 4.38E-06