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 mr1305 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
vg0325696417 sf0325694435 3 25696417 5.28E-37 5.95E-33
vg0400345487 sf0400344487 4 345487 2.24E-20 1.15E-15
vg1121970827 sf1121504698 11 21970827 1.06E-14 5.26E-10
vg0229389860 sf0229383991 2 29389860 2.95E-14 1.07E-09
vg1004789770 sf1004806307 10 4789770 4.89E-14 2.92E-11
vg0625912245 sf0625911248 6 25912245 7.71E-13 2.36E-09
vg0609841754 sf0609840755 6 9841754 8.88E-13 1.19E-10
vg0202749886 sf0202749884 2 2749886 4.14E-12 1.90E-08
vg0415028838 sf0415019552 4 15028838 5.46E-12 1.46E-10
vg0221444241 sf0221438373 2 21444241 6.99E-12 6.67E-09
vg1012888857 sf1012817672 10 12888857 3.52E-11 2.40E-10
vg1005573976 sf1005590514 10 5573976 3.55E-11 1.36E-08
vg0235815991 sf0235810122 2 35815991 1.98E-10 2.76E-08
vg0310704341 sf0310703257 3 10704341 2.81E-10 2.02E-08
vg0304791741 sf0304790743 3 4791741 3.19E-10 3.64E-08
vg0322796391 sf0322794880 3 22796391 5.82E-10 6.92E-09
vg0207824124 sf0207824123 2 7824124 5.20E-09 2.61E-09
vg0227505093 sf0227499224 2 27505093 5.73E-09 9.59E-08
vg0216273226 sf0216267356 2 16273226 6.12E-09 2.15E-08
vg0400034660 sf0400033660 4 34660 2.39E-08 4.65E-08