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 mr1233 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
vg0719302457 sf0719301464 7 19302457 1.49E-32 1.53E-22
vg0719188664 sf0719187671 7 19188664 4.97E-30 1.73E-23
vg0719051231 sf0719050238 7 19051231 9.83E-22 2.27E-19
vg0228211032 sf0228205163 2 28211032 3.04E-19 1.67E-06
vg0719057980 sf0719056987 7 19057980 3.49E-16 4.40E-16
vg0336362940 sf0336355810 3 36362940 1.53E-15 NA
vg0718924722 sf0718923729 7 18924722 3.08E-15 NA
vg0719514240 sf0719513247 7 19514240 1.40E-14 7.66E-10
vg0711196143 sf0711195149 7 11196143 6.88E-13 4.10E-06
vg0406419424 sf0406414864 4 6419424 8.51E-12 NA
vg0719323752 sf0719322759 7 19323752 NA 4.33E-11
vg0718961880 sf0718960887 7 18961880 NA 8.56E-10
vg0719466615 sf0719465622 7 19466615 NA 4.33E-09
vg0719153328 sf0719152335 7 19153328 NA 1.03E-08
vg0719105731 sf0719104738 7 19105731 NA 5.28E-08
vg1216729892 sf1216723846 12 16729892 NA 7.35E-08
vg0431516011 sf0431330910 4 31516011 NA 5.17E-07
vg0209435787 sf0209435785 2 9435787 NA 3.50E-06
vg1207833484 sf1207830890 12 7833484 NA 4.40E-06