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 mr1671 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
vg0334637220 sf0334630090 3 34637220 7.52E-18 9.81E-18
vg0804768881 sf0804767884 8 4768881 5.69E-09 NA
vg0324810224 sf0324808303 3 24810224 7.86E-09 NA
vg0527396336 sf0527333692 5 27396336 3.05E-08 NA
vg0305010329 sf0305009331 3 5010329 3.33E-08 1.66E-06
vg0304992244 sf0304991246 3 4992244 8.43E-08 8.02E-07
vg0804698573 sf0804697576 8 4698573 1.32E-07 1.41E-06
vg1205330045 sf1205329031 12 5330045 4.88E-06 NA
vg0334285053 sf0334277923 3 34285053 7.17E-06 3.91E-07
vg0334677267 sf0334670137 3 34677267 NA 3.55E-07
vg0309199102 sf0309198038 3 9199102 NA 8.27E-07
vg0304365624 sf0304364626 3 4365624 NA 1.37E-06
vg0318823675 sf0318822435 3 18823675 NA 4.09E-06