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 mr1818 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
vg0217109505 sf0217103635 2 17109505 2.30E-46 1.39E-22
vg0216789715 sf0216783845 2 16789715 1.22E-44 3.86E-23
vg1220336354 sf1220307796 12 20336354 1.21E-23 1.08E-07
vg1220336338 sf1220307780 12 20336338 1.39E-22 4.02E-08
vg1015182556 sf1015111324 10 15182556 2.17E-22 7.85E-06
vg1226816492 sf1226782891 12 26816492 1.29E-19 6.38E-06
vg0723337151 sf0723336158 7 23337151 5.35E-19 NA
vg0725840534 sf0725839540 7 25840534 7.32E-18 7.48E-09
vg0217940995 sf0217935126 2 17940995 1.47E-16 4.51E-10
vg1108225523 sf1108220133 11 8225523 3.38E-16 3.18E-06
vg0217144699 sf0217138829 2 17144699 8.86E-15 1.05E-17
vg1204392945 sf1204391933 12 4392945 2.07E-13 4.47E-06
vg0217474288 sf0217468418 2 17474288 5.59E-13 1.27E-08
vg0217497082 sf0217491212 2 17497082 1.58E-12 4.59E-09
vg0217524100 sf0217518230 2 17524100 NA 3.67E-08
vg0118878498 sf0118877453 1 18878498 NA 1.89E-06
vg0216658829 sf0216652959 2 16658829 NA 2.30E-06
vg0217861925 sf0217856056 2 17861925 NA 2.36E-06
vg1216728542 sf1216722496 12 16728542 NA 2.86E-06