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 mr1663 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
vg0902278490 sf0902277490 9 2278490 5.22E-09 1.86E-07
vg0630441706 sf0630440708 6 30441706 1.76E-08 2.83E-07
vg0630443303 sf0630442305 6 30443303 2.49E-08 3.93E-07
vg0801877389 sf0801876392 8 1877389 6.30E-08 1.84E-06
vg0801788465 sf0801787468 8 1788465 7.06E-08 1.53E-06
vg0726559146 sf0726558152 7 26559146 7.20E-08 1.24E-07
vg0420718113 sf0420546156 4 20718113 9.37E-08 8.42E-07
vg0808428148 sf0808427152 8 8428148 1.29E-07 1.60E-07
vg0607659813 sf0607658814 6 7659813 1.45E-07 2.35E-06
vg0223525077 sf0223519208 2 23525077 1.55E-07 3.20E-07
vg1105850609 sf1105846361 11 5850609 7.98E-07 4.65E-06
vg0123891450 sf0123890406 1 23891450 1.68E-06 2.90E-06
vg0805623272 sf0805622275 8 5623272 3.53E-06 3.91E-06
vg1020531763 sf1020460242 10 20531763 8.12E-06 1.12E-07
vg0801697883 sf0801696886 8 1697883 NA 8.67E-07
vg0718397736 sf0718396743 7 18397736 NA 2.28E-06
vg0430479443 sf0430294321 4 30479443 NA 3.00E-06
vg0805992743 sf0805991746 8 5992743 NA 3.04E-06
vg0417840360 sf0417668400 4 17840360 NA 3.20E-06