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 mr1037 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
vg0402396092 sf0402391687 4 2396092 1.77E-42 8.93E-12
vg0205749844 sf0205749844 2 5749844 9.24E-34 NA
vg0314422675 sf0314421364 3 14422675 5.31E-33 3.23E-06
vg0334386865 sf0334379735 3 34386865 4.87E-32 NA
vg0230309897 sf0230304028 2 30309897 5.52E-32 NA
vg0334560863 sf0334553733 3 34560863 1.49E-27 3.77E-06
vg0402374019 sf0402369614 4 2374019 NA 2.51E-08
vg0921456103 sf0921455622 9 21456103 NA 5.80E-08
vg0921456056 sf0921455575 9 21456056 NA 1.19E-07
vg0801631583 sf0801630585 8 1631583 NA 5.45E-07
vg0816065682 sf0816062968 8 16065682 NA 2.81E-06
vg0135309354 sf0135308311 1 35309354 NA 3.82E-06
vg0816681021 sf0816678307 8 16681021 NA 6.63E-06