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 mr1882 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
vg0314128708 sf0314127397 3 14128708 2.41E-08 8.14E-06
vg0123720143 sf0123719099 1 23720143 2.89E-08 NA
vg0100935871 sf0100934871 1 935871 2.91E-08 NA
vg0405708494 sf0405703933 4 5708494 3.64E-08 NA
vg0300230192 sf0300229192 3 230192 4.74E-08 NA
vg0406480943 sf0406476386 4 6480943 1.32E-07 NA
vg1216702317 sf1216696271 12 16702317 4.43E-06 6.76E-06
vg0907680153 sf0907679153 9 7680153 6.28E-06 9.50E-06
vg0709672527 sf0709671533 7 9672527 NA 6.62E-06