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 mr1034 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
vg0304178129 sf0304177131 3 4178129 9.65E-10 2.38E-06
vg1211905124 sf1211902459 12 11905124 5.04E-09 NA
vg0401347470 sf0401343020 4 1347470 4.59E-08 3.54E-06
vg0433675778 sf0433490661 4 33675778 4.95E-08 NA
vg1208521712 sf1208519119 12 8521712 6.08E-08 NA
vg1118460774 sf1117994633 11 18460774 6.42E-08 1.56E-06
vg0433930554 sf0433745450 4 33930554 1.05E-07 3.79E-06
vg1006058550 sf1006075088 10 6058550 1.28E-07 1.60E-06
vg0224289132 sf0224283263 2 24289132 2.51E-06 4.04E-06