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 mr1478 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
vg0727995401 sf0727994408 7 27995401 2.51E-11 1.89E-06
vg1217611967 sf1217605922 12 17611967 7.48E-10 NA
vg0138112582 sf0138111539 1 38112582 5.46E-09 NA
vg0613999068 sf0613998069 6 13999068 7.78E-09 NA
vg0130089725 sf0130088680 1 30089725 1.09E-08 NA
vg0227788767 sf0227782898 2 27788767 4.36E-08 NA
vg0502125341 sf0502125315 5 2125341 1.53E-07 5.45E-08
vg0614122855 sf0614121856 6 14122855 1.60E-07 3.65E-06
vg0518363321 sf0518302807 5 18363321 1.91E-06 4.39E-07
vg1121160624 sf1120694503 11 21160624 2.66E-06 NA
vg0110162754 sf0110161730 1 10162754 NA 2.48E-06
vg0110016398 sf0110015374 1 10016398 NA 4.69E-06
vg0610862201 sf0610861202 6 10862201 NA 7.24E-06