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 mr1592 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
vg0222742146 sf0222736277 2 22742146 6.04E-20 5.44E-14
vg0223747273 sf0223741404 2 23747273 3.50E-12 1.71E-06
vg0223663746 sf0223657877 2 23663746 2.08E-11 1.24E-06
vg0224639328 sf0224633459 2 24639328 4.17E-09 NA
vg0908732615 sf0908731614 9 8732615 4.55E-09 NA
vg0226061785 sf0226055916 2 26061785 5.59E-09 NA
vg0324647482 sf0324645561 3 24647482 1.36E-07 1.02E-06
vg0804771202 sf0804770205 8 4771202 2.46E-06 NA
vg0421497689 sf0421325740 4 21497689 6.75E-06 NA
vg0610105747 sf0610104748 6 10105747 NA 9.71E-07
vg0222700671 sf0222694802 2 22700671 NA 3.65E-06
vg0610106990 sf0610105991 6 10106990 NA 7.66E-06