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 mr1438 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
vg1122410940 sf1121944811 11 22410940 3.05E-10 3.79E-06
vg0130277591 sf0130276546 1 30277591 1.70E-09 NA
vg0907659025 sf0907658025 9 7659025 2.30E-09 NA
vg0142314165 sf0142313121 1 42314165 5.64E-09 NA
vg1202888107 sf1202887109 12 2888107 4.01E-08 NA
vg0618221570 sf0618220573 6 18221570 2.68E-07 NA
vg0220279272 sf0220273404 2 20279272 5.78E-07 NA
vg0226828976 sf0226823107 2 26828976 NA 1.87E-06
vg0122965630 sf0122964586 1 22965630 NA 2.75E-06