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 mr1774 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
vg0701643483 sf0701642484 7 1643483 4.20E-10 NA
vg1221154570 sf1221121116 12 21154570 4.49E-10 3.21E-06
vg0206319805 sf0206319805 2 6319805 5.53E-10 9.86E-06
vg1013275525 sf1013204295 10 13275525 1.14E-09 1.23E-06
vg0528509683 sf0528447038 5 28509683 1.38E-09 NA
vg0414193101 sf0414183817 4 14193101 2.09E-08 2.50E-06
vg0406861879 sf0406857324 4 6861879 NA 3.19E-06
vg1217175447 sf1217169402 12 17175447 NA 3.38E-06
vg0406862378 sf0406857823 4 6862378 NA 4.19E-06
vg1216280518 sf1216277814 12 16280518 NA 5.51E-06