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 mr1587 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
vg1215970377 sf1215967673 12 15970377 1.38E-10 8.32E-09
vg1209292727 sf1209290137 12 9292727 1.70E-10 5.66E-09
vg1215990882 sf1215988178 12 15990882 7.18E-10 5.39E-09
vg1210584952 sf1210582365 12 10584952 1.30E-09 3.79E-08
vg0336268568 sf0336261438 3 36268568 2.40E-09 9.17E-06
vg0422487302 sf0422302189 4 22487302 2.66E-09 NA
vg0134332405 sf0134331362 1 34332405 4.36E-08 NA
vg0419753293 sf0419581328 4 19753293 8.00E-08 3.80E-06
vg1223872959 sf1223839412 12 23872959 9.54E-08 2.16E-06
vg1220914154 sf1220880703 12 20914154 1.61E-07 2.00E-06
vg0805903403 sf0805902406 8 5903403 1.28E-06 4.01E-06
vg0105278554 sf0105277554 1 5278554 1.94E-06 6.26E-07
vg0805495214 sf0805494217 8 5495214 NA 2.36E-06