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 mr1825 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
vg0229264221 sf0229258352 2 29264221 1.04E-38 NA
vg0709984493 sf0709983499 7 9984493 1.73E-37 NA
vg0142954896 sf0142953852 1 42954896 7.12E-37 NA
vg0119202868 sf0119201823 1 19202868 8.67E-37 NA
vg0233357493 sf0233351624 2 33357493 9.04E-37 NA
vg0802264279 sf0802263282 8 2264279 5.68E-33 3.76E-06
vg0424093683 sf0423908544 4 24093683 3.51E-31 NA
vg0434817544 sf0434632435 4 34817544 2.56E-30 4.57E-06
vg0130584881 sf0130583837 1 30584881 NA 4.13E-08
vg1008183244 sf1008112106 10 8183244 NA 3.13E-07
vg0233348766 sf0233342897 2 33348766 NA 3.10E-06
vg0607963440 sf0607962441 6 7963440 NA 4.13E-06
vg1005760390 sf1005776928 10 5760390 NA 4.23E-06
vg1006088409 sf1006104946 10 6088409 NA 4.69E-06
vg0233380528 sf0233374659 2 33380528 NA 5.88E-06
vg1216282451 sf1216279747 12 16282451 NA 6.63E-06