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 mr1125 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
vg0235337136 sf0235331267 2 35337136 7.24E-16 7.12E-10
vg0235365192 sf0235359323 2 35365192 9.16E-14 3.87E-09
vg0523892684 sf0523830105 5 23892684 4.20E-12 1.88E-08
vg1108660993 sf1108655603 11 8660993 1.69E-11 5.94E-07
vg1125345786 sf1124879626 11 25345786 2.55E-11 5.24E-08
vg1127487577 sf1127015964 11 27487577 5.68E-11 NA
vg0914935450 sf0914934449 9 14935450 2.86E-10 3.36E-06
vg0918661273 sf0918660272 9 18661273 4.84E-10 3.34E-06
vg0235259229 sf0235253360 2 35259229 1.77E-09 3.17E-06
vg0207527515 sf0207527515 2 7527515 2.93E-09 4.54E-06
vg0112458126 sf0112457100 1 12458126 5.61E-09 1.01E-06
vg0102429074 sf0102428074 1 2429074 9.16E-08 NA
vg1204323650 sf1204322638 12 4323650 1.13E-07 2.25E-06
vg0910969166 sf0910968165 9 10969166 NA 4.15E-06