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 mr1328 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
vg1012420785 sf1012349600 10 12420785 4.54E-12 NA
vg0308388246 sf0308387184 3 8388246 5.24E-11 NA
vg1012244370 sf1012173185 10 12244370 5.37E-11 3.53E-07
vg0608277816 sf0608276817 6 8277816 7.52E-11 NA
vg0431530955 sf0431345854 4 31530955 2.05E-10 NA
vg0500806196 sf0500806178 5 806196 3.07E-10 NA
vg0431515573 sf0431330472 4 31515573 7.79E-09 3.49E-06
vg0224478551 sf0224472682 2 24478551 2.79E-07 4.42E-06
vg1218088617 sf1218060053 12 18088617 NA 1.16E-06
vg0308378299 sf0308377237 3 8378299 NA 2.12E-06
vg0827004405 sf0827001691 8 27004405 NA 2.67E-06
vg0103252222 sf0103251222 1 3252222 NA 3.53E-06
vg0329497105 sf0329490145 3 29497105 NA 8.49E-06
vg0820146322 sf0820143609 8 20146322 NA 8.86E-06