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 mr1777 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
vg0528836237 sf0528773592 5 28836237 4.42E-08 4.42E-08
vg0300939247 sf0300938245 3 939247 8.50E-08 8.51E-08
vg0915815139 sf0915814138 9 15815139 3.06E-07 3.06E-07
vg1206186379 sf1206185270 12 6186379 3.26E-07 3.27E-07
vg0207699992 sf0207699991 2 7699992 6.51E-07 6.52E-07
vg0300761695 sf0300760693 3 761695 1.10E-06 1.10E-06
vg0316482661 sf0316481306 3 16482661 1.16E-06 1.17E-06
vg0805992743 sf0805991746 8 5992743 1.32E-06 1.32E-06
vg0335297514 sf0335290383 3 35297514 1.42E-06 1.42E-06
vg0721356842 sf0721355849 7 21356842 1.42E-06 1.42E-06
vg1107881424 sf1107877169 11 7881424 1.42E-06 1.42E-06
vg0315029385 sf0315028032 3 15029385 1.55E-06 1.56E-06
vg1208280451 sf1208277857 12 8280451 1.77E-06 1.77E-06
vg0431387810 sf0431202708 4 31387810 2.89E-06 2.90E-06
vg0316269128 sf0316267775 3 16269128 3.13E-06 3.14E-06
vg1210647989 sf1210645402 12 10647989 4.02E-06 4.03E-06
vg0722226606 sf0722225613 7 22226606 4.16E-06 4.16E-06
vg1216720660 sf1216714614 12 16720660 4.39E-06 4.40E-06
vg0431515534 sf0431330433 4 31515534 4.58E-06 4.57E-06
vg1217304013 sf1217297968 12 17304013 4.84E-06 4.85E-06