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 mr1798 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
vg0402389835 sf0402385430 4 2389835 1.52E-138 7.35E-39
vg0205801196 sf0205801196 2 5801196 1.48E-87 NA
vg0708600682 sf0708599687 7 8600682 1.30E-84 NA
vg0428607419 sf0428422270 4 28607419 1.65E-84 NA
vg0334548303 sf0334541173 3 34548303 3.01E-82 NA
vg0317737568 sf0317736350 3 17737568 4.51E-68 NA
vg0402406368 sf0402401963 4 2406368 NA 1.23E-32
vg1010719593 sf1010648414 10 10719593 NA 5.78E-16
vg0401972146 sf0401967742 4 1972146 NA 7.76E-13
vg0402432258 sf0402427853 4 2432258 NA 9.03E-12
vg0402455074 sf0402450671 4 2455074 NA 2.62E-11
vg0402032567 sf0402028163 4 2032567 NA 6.97E-11
vg0402386328 sf0402381923 4 2386328 NA 6.05E-10
vg0401992281 sf0401987877 4 1992281 NA 1.20E-09
vg0403660277 sf0403655881 4 3660277 NA 1.25E-09
vg0402465230 sf0402460828 4 2465230 NA 2.75E-09
vg0402468342 sf0402463940 4 2468342 NA 5.42E-09
vg0402448500 sf0402444096 4 2448500 NA 4.13E-08
vg0516236934 sf0516179416 5 16236934 NA 5.99E-08
vg0402053743 sf0402049339 4 2053743 NA 7.24E-08
vg0401901910 sf0401897506 4 1901910 NA 8.20E-08
vg0404609763 sf0404605366 4 4609763 NA 1.38E-07
vg0402019968 sf0402015564 4 2019968 NA 1.79E-07
vg0402476520 sf0402472118 4 2476520 NA 3.27E-07
vg0403840443 sf0403836047 4 3840443 NA 3.44E-07
vg0402048811 sf0402044407 4 2048811 NA 3.64E-07
vg0404311033 sf0404306639 4 4311033 NA 7.48E-07
vg0402501639 sf0402497241 4 2501639 NA 9.23E-07