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 mr1580 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
vg0229268619 sf0229262750 2 29268619 2.82E-40 NA
vg0709984493 sf0709983499 7 9984493 1.82E-38 NA
vg0142954896 sf0142953852 1 42954896 3.18E-38 NA
vg0119206707 sf0119205662 1 19206707 9.06E-38 NA
vg0823905607 sf0823902893 8 23905607 2.82E-37 NA
vg0709679219 sf0709678225 7 9679219 4.13E-34 NA
vg0801924208 sf0801923211 8 1924208 1.09E-33 NA
vg0425623927 sf0425438788 4 25623927 NA 4.34E-07
vg1216282451 sf1216279747 12 16282451 NA 4.39E-07
vg1008183244 sf1008112106 10 8183244 NA 5.41E-07
vg0130584881 sf0130583837 1 30584881 NA 9.90E-07
vg1005741077 sf1005757615 10 5741077 NA 1.03E-06
vg0607961607 sf0607960608 6 7961607 NA 1.15E-06
vg0425517267 sf0425332127 4 25517267 NA 1.18E-06
vg0130722455 sf0130721411 1 30722455 NA 1.38E-06
vg0425698075 sf0425512937 4 25698075 NA 4.24E-06
vg0105763607 sf0105762607 1 5763607 NA 4.80E-06
vg0607963440 sf0607962441 6 7963440 NA 7.85E-06