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 mr1189 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
vg1219172886 sf1219144356 12 19172886 9.60E-08 NA
vg0816220663 sf0816217949 8 16220663 2.67E-07 2.64E-06
vg0919810818 sf0919810337 9 19810818 2.37E-06 NA
vg0121835877 sf0121834832 1 21835877 4.28E-06 4.12E-06
vg0916243238 sf0916242237 9 16243238 NA 2.98E-06
vg0912040576 sf0912039575 9 12040576 NA 4.94E-06