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 mr1005 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
vg0501245720 sf0501245704 5 1245720 1.62E-08 6.41E-09
vg0314683652 sf0314682339 3 14683652 3.86E-08 1.13E-07
vg0212300877 sf0212300873 2 12300877 4.70E-08 1.50E-07
vg0614462670 sf0614461671 6 14462670 5.58E-08 9.69E-06
vg0602961865 sf0602960866 6 2961865 8.31E-08 3.06E-06
vg1109603153 sf1109597730 11 9603153 1.72E-07 8.25E-07
vg0220043147 sf0220037279 2 20043147 1.98E-07 5.52E-10
vg0800938996 sf0800937998 8 938996 2.96E-07 6.39E-07
vg0421045057 sf0420873111 4 21045057 3.26E-07 5.84E-07
vg0208229343 sf0208229342 2 8229343 1.33E-06 4.84E-08
vg0221671440 sf0221665571 2 21671440 1.61E-06 7.04E-07
vg1214406518 sf1214403859 12 14406518 7.37E-06 7.90E-07
vg0706877418 sf0706876423 7 6877418 NA 2.97E-09
vg1001623967 sf1001622944 10 1623967 NA 6.47E-08
vg0503966024 sf0503966001 5 3966024 NA 2.02E-07
vg0503822720 sf0503822697 5 3822720 NA 2.16E-07
vg0725477178 sf0725476184 7 25477178 NA 2.22E-07
vg0716176808 sf0716175815 7 16176808 NA 3.04E-07
vg0713636558 sf0713635565 7 13636558 NA 8.37E-07
vg0600114214 sf0600113214 6 114214 NA 1.18E-06
vg0808604844 sf0808603848 8 8604844 NA 1.72E-06
vg0809300703 sf0809299707 8 9300703 NA 2.47E-06
vg1015794903 sf1015723673 10 15794903 NA 2.49E-06