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 mr1347 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
vg0429947446 sf0429762313 4 29947446 2.64E-16 8.99E-11
vg0429933325 sf0429748192 4 29933325 3.78E-16 5.12E-11
vg0804327457 sf0804326460 8 4327457 1.41E-10 9.74E-13
vg0804324100 sf0804323103 8 4324100 4.54E-10 9.42E-13
vg0430022022 sf0429836891 4 30022022 3.09E-09 4.92E-06
vg1104746758 sf1104742660 11 4746758 4.82E-09 NA
vg0430452456 sf0430267333 4 30452456 8.36E-09 1.94E-06
vg1207257056 sf1207254463 12 7257056 1.46E-08 1.62E-06
vg0131964524 sf0131963480 1 31964524 2.39E-07 NA
vg0804315269 sf0804314272 8 4315269 6.67E-07 4.30E-11
vg0102859069 sf0102858069 1 2859069 6.76E-07 1.18E-06
vg0311016054 sf0311014772 3 11016054 NA 3.77E-06
vg0419568634 sf0419396669 4 19568634 NA 4.03E-06