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 mr1619 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
vg0222744532 sf0222738663 2 22744532 5.01E-16 5.83E-09
vg0204877627 sf0204877624 2 4877627 6.17E-10 NA
vg0324327479 sf0324325558 3 24327479 6.81E-10 2.90E-08
vg0223943227 sf0223937358 2 23943227 9.38E-10 NA
vg0615245670 sf0615244671 6 15245670 2.90E-09 4.77E-06
vg0222211789 sf0222205920 2 22211789 3.64E-09 2.77E-07
vg1009567423 sf1009496244 10 9567423 4.35E-09 4.11E-07
vg0406948268 sf0406943536 4 6948268 6.22E-09 2.06E-06
vg0615245465 sf0615244466 6 15245465 7.47E-09 4.22E-06
vg0406948399 sf0406943667 4 6948399 2.98E-08 1.69E-06
vg1010618338 sf1010547159 10 10618338 4.80E-08 NA
vg0222852276 sf0222846407 2 22852276 7.28E-08 3.48E-06
vg0406592386 sf0406587830 4 6592386 1.36E-07 1.73E-06
vg0222023649 sf0222017780 2 22023649 1.45E-07 1.11E-06
vg0618618072 sf0618617075 6 18618072 1.61E-07 1.77E-06
vg0407665649 sf0407660916 4 7665649 5.32E-07 6.07E-10
vg0225217180 sf0225211311 2 25217180 7.06E-07 3.38E-06
vg0813085446 sf0813083076 8 13085446 3.21E-06 2.92E-06
vg0909042994 sf0909041993 9 9042994 3.82E-06 5.51E-07
vg1205884419 sf1205883401 12 5884419 NA 4.23E-06
vg1113530105 sf1113066427 11 13530105 NA 4.43E-06
vg0112525167 sf0112524141 1 12525167 NA 4.49E-06