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 mr1344 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
vg0137432575 sf0137431532 1 37432575 1.12E-06 NA
vg1221086538 sf1221053088 12 21086538 1.27E-06 3.49E-06
vg1017360881 sf1017289654 10 17360881 1.84E-06 5.57E-07
vg0420812196 sf0420640239 4 20812196 2.28E-06 4.58E-06
vg0407332240 sf0407327510 4 7332240 9.88E-06 3.07E-06
vg1016084462 sf1016013234 10 16084462 NA 3.77E-06