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 mr1388 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
vg1217370492 sf1217364447 12 17370492 2.77E-11 2.84E-09
vg0222244751 sf0222238882 2 22244751 1.54E-10 2.15E-08
vg0821373981 sf0821371268 8 21373981 1.17E-08 1.01E-06
vg0329268317 sf0329261357 3 29268317 1.78E-08 5.14E-06
vg0827664904 sf0827662190 8 27664904 4.72E-08 7.83E-06
vg0124774093 sf0124773049 1 24774093 NA 6.42E-07
vg0124727516 sf0124726472 1 24727516 NA 7.24E-07
vg0820710287 sf0820707574 8 20710287 NA 1.04E-06
vg0217328131 sf0217322261 2 17328131 NA 3.07E-06