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 mr1733 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
vg0304801695 sf0304800697 3 4801695 1.41E-08 NA
vg0429127308 sf0428942168 4 29127308 7.58E-08 NA
vg0427436094 sf0427250958 4 27436094 8.53E-08 NA
vg0216865447 sf0216859577 2 16865447 6.79E-07 2.62E-06
vg0507921491 sf0507921432 5 7921491 8.04E-07 1.58E-06
vg0202090631 sf0202090631 2 2090631 1.23E-06 3.17E-06
vg0304752239 sf0304751241 3 4752239 3.13E-06 4.00E-06
vg0400771041 sf0400770041 4 771041 3.16E-06 3.49E-06
vg0410967768 sf0410958469 4 10967768 4.29E-06 1.11E-06
vg0628044583 sf0628043585 6 28044583 5.18E-06 9.57E-06
vg0423327436 sf0423142291 4 23327436 8.87E-06 NA