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 mr1362 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
vg0317860149 sf0317858931 3 17860149 1.23E-07 1.23E-07
vg0816292104 sf0816289390 8 16292104 2.15E-07 2.15E-07
vg0320452783 sf0320451294 3 20452783 2.57E-07 2.56E-07
vg0504475373 sf0504475350 5 4475373 3.48E-07 3.48E-07
vg0430367665 sf0430182542 4 30367665 3.56E-07 3.56E-07
vg1109816182 sf1109810759 11 9816182 4.72E-07 4.72E-07
vg0416336988 sf0416165021 4 16336988 9.75E-07 9.75E-07
vg0423665696 sf0423480553 4 23665696 1.80E-06 1.80E-06
vg0805049102 sf0805048105 8 5049102 1.89E-06 1.89E-06
vg1208212826 sf1208210231 12 8212826 2.50E-06 2.50E-06
vg0212092329 sf0212092325 2 12092329 3.20E-06 3.20E-06
vg0609793222 sf0609792223 6 9793222 3.71E-06 3.71E-06
vg1216118354 sf1216115650 12 16118354 4.78E-06 4.78E-06