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 mr1264 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
vg0719140447 sf0719139454 7 19140447 5.47E-35 2.85E-13
vg0719051231 sf0719050238 7 19051231 4.00E-34 5.65E-18
vg0719208938 sf0719207945 7 19208938 1.65E-32 1.26E-09
vg0305696088 sf0305695088 3 5696088 8.93E-30 NA
vg0706906002 sf0706905007 7 6906002 3.26E-29 NA
vg0315157953 sf0315156600 3 15157953 3.47E-28 1.74E-06
vg0613002491 sf0613001492 6 13002491 1.39E-27 NA
vg0315197013 sf0315195660 3 15197013 1.39E-26 3.65E-07
vg0719449907 sf0719448914 7 19449907 NA 5.20E-11
vg0719057980 sf0719056987 7 19057980 NA 1.65E-08
vg0719129945 sf0719128952 7 19129945 NA 1.94E-08
vg0329561125 sf0329554165 3 29561125 NA 3.07E-08
vg0126418162 sf0126417118 1 26418162 NA 5.21E-07
vg0126442845 sf0126441801 1 26442845 NA 8.72E-07
vg1204022544 sf1204021532 12 4022544 NA 1.29E-06
vg0718961965 sf0718960972 7 18961965 NA 1.90E-06
vg0719140498 sf0719139505 7 19140498 NA 2.07E-06
vg0909775480 sf0909774479 9 9775480 NA 2.29E-06
vg0720529894 sf0720528901 7 20529894 NA 3.24E-06
vg1004891006 sf1004907543 10 4891006 NA 3.45E-06
vg1100598516 sf1100597519 11 598516 NA 3.85E-06
vg1214515607 sf1214512948 12 14515607 NA 4.03E-06
vg1214515514 sf1214512855 12 14515514 NA 4.75E-06
vg0406753488 sf0406748934 4 6753488 NA 4.80E-06