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
vg0719133785 sf0719132792 7 19133785 9.61E-13 1.37E-09
vg0719011406 sf0719010413 7 19011406 1.11E-12 1.04E-10
vg0719090536 sf0719089543 7 19090536 1.48E-09 2.75E-09
vg1202102394 sf1202101392 12 2102394 2.20E-09 1.30E-07
vg0719136336 sf0719135343 7 19136336 3.25E-09 1.14E-06
vg1004296464 sf1004313002 10 4296464 7.99E-09 3.66E-07
vg0315179733 sf0315178380 3 15179733 5.79E-08 NA
vg0412457639 sf0412448354 4 12457639 2.13E-06 3.30E-06
vg1009450763 sf1009379584 10 9450763 4.76E-06 1.93E-06
vg0229023414 sf0229017545 2 29023414 5.47E-06 NA
vg1009407594 sf1009336415 10 9407594 5.71E-06 5.98E-06
vg1104978992 sf1104974803 11 4978992 9.83E-06 NA
vg0718985954 sf0718984961 7 18985954 NA 8.89E-07