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 mr1650 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
vg0803653778 sf0803652781 8 3653778 2.79E-11 1.52E-08
vg0803656534 sf0803655537 8 3656534 4.62E-11 1.48E-08
vg0134272325 sf0134271282 1 34272325 2.23E-10 3.37E-08
vg0402180766 sf0402176361 4 2180766 1.19E-09 2.25E-06
vg0402180792 sf0402176387 4 2180792 2.11E-09 2.72E-06
vg0401346827 sf0401342377 4 1346827 2.58E-09 1.14E-06
vg0134084206 sf0134083162 1 34084206 6.89E-09 4.30E-07
vg0618798718 sf0618797721 6 18798718 1.06E-08 1.99E-06
vg0626321316 sf0626320319 6 26321316 2.03E-08 NA
vg1226678487 sf1226644883 12 26678487 5.40E-08 3.63E-06
vg0711760152 sf0711759158 7 11760152 1.21E-07 2.64E-06
vg1117462451 sf1116996306 11 17462451 1.46E-06 3.03E-06