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 mr1089 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
vg0216822884 sf0216817014 2 16822884 1.22E-58 8.97E-24
vg0216699507 sf0216693637 2 16699507 2.60E-58 6.85E-12
vg0216735359 sf0216729489 2 16735359 1.52E-57 2.45E-13
vg0216898142 sf0216892272 2 16898142 1.39E-56 1.66E-13
vg0310117701 sf0310116637 3 10117701 2.43E-54 NA
vg0720349785 sf0720348792 7 20349785 3.41E-53 NA
vg0129124737 sf0129123692 1 29124737 4.27E-51 NA
vg0718840106 sf0718839113 7 18840106 1.82E-45 9.20E-07
vg0407135809 sf0407131079 4 7135809 1.12E-42 2.95E-06
vg0217137734 sf0217131864 2 17137734 NA 4.70E-11
vg0812023942 sf0812022947 8 12023942 NA 6.50E-09
vg0130732040 sf0130730996 1 30732040 NA 1.94E-08
vg0900337327 sf0900336327 9 337327 NA 6.42E-08
vg0216472199 sf0216466329 2 16472199 NA 3.85E-07
vg0819589271 sf0819586558 8 19589271 NA 6.68E-07
vg0212179963 sf0212179959 2 12179963 NA 7.54E-07
vg0130832570 sf0130831526 1 30832570 NA 7.60E-07
vg0231328780 sf0231322911 2 31328780 NA 8.71E-07
vg1114473442 sf1114009759 11 14473442 NA 1.57E-06
vg1108349674 sf1108344284 11 8349674 NA 2.60E-06
vg1105770829 sf1105766581 11 5770829 NA 3.19E-06
vg0703938539 sf0703937540 7 3938539 NA 8.04E-06