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 mr1959 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
vg1000583028 sf1000582004 10 583028 2.48E-23 9.59E-18
vg1125100181 sf1124634021 11 25100181 2.42E-15 5.81E-09
vg1011400274 sf1011329093 10 11400274 2.63E-15 2.43E-07
vg1125113372 sf1124647212 11 25113372 1.89E-14 1.43E-10
vg0528146502 sf0528083857 5 28146502 2.55E-14 1.01E-08
vg0700359527 sf0700358527 7 359527 1.53E-13 3.28E-07
vg1011080958 sf1011009778 10 11080958 3.77E-13 1.83E-07
vg1211822486 sf1211819822 12 11822486 2.11E-12 4.51E-06
vg0129913271 sf0129912226 1 29913271 4.63E-11 2.87E-06
vg0629161828 sf0629160830 6 29161828 6.00E-11 1.56E-06
vg1002061060 sf1002060037 10 2061060 3.87E-10 2.60E-06
vg1000730968 sf1000729944 10 730968 2.22E-09 4.80E-07
vg1125046291 sf1124580131 11 25046291 NA 2.07E-12
vg1125127060 sf1124660900 11 25127060 NA 3.97E-12
vg1010925312 sf1010854132 10 10925312 NA 3.98E-06
vg1122507712 sf1122041583 11 22507712 NA 4.21E-06
vg0139173593 sf0139172550 1 39173593 NA 4.46E-06
vg1000754147 sf1000753123 10 754147 NA 4.58E-06
vg1200149931 sf1200148931 12 149931 NA 4.78E-06
vg0501865585 sf0501865567 5 1865585 NA 4.84E-06