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 mr1598 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
vg0918922771 sf0918921771 9 18922771 3.52E-23 9.53E-16
vg0918923624 sf0918922624 9 18923624 4.08E-23 7.46E-16
vg1102472614 sf1102468518 11 2472614 1.57E-12 1.64E-07
vg0917226024 sf0917225023 9 17226024 2.34E-11 3.41E-06
vg0919898501 sf0919898020 9 19898501 4.61E-11 2.89E-06
vg0919904873 sf0919904392 9 19904873 6.41E-11 2.77E-06
vg0919230563 sf0919230153 9 19230563 8.04E-11 3.75E-06
vg1005421909 sf1005438446 10 5421909 1.98E-09 3.62E-06
vg1102879043 sf1102874947 11 2879043 2.59E-07 NA
vg0801987032 sf0801986035 8 1987032 4.95E-06 NA
vg0918711324 sf0918710324 9 18711324 8.51E-06 1.77E-07
vg0214641768 sf0214635898 2 14641768 NA 1.06E-06