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 mr1793 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
vg0919907455 sf0919906974 9 19907455 1.07E-14 1.75E-10
vg0919906368 sf0919905887 9 19906368 2.31E-14 2.28E-11
vg0219567311 sf0219561443 2 19567311 2.93E-10 NA
vg0219348866 sf0219342998 2 19348866 4.76E-10 4.52E-06
vg0502469018 sf0502468994 5 2469018 1.60E-09 NA
vg0919955235 sf0919954754 9 19955235 1.87E-09 1.47E-06
vg0505805966 sf0505805904 5 5805966 2.24E-09 5.86E-06
vg0920993132 sf0920992651 9 20993132 2.77E-09 5.04E-06
vg0919897221 sf0919896740 9 19897221 9.35E-09 6.38E-07
vg0818493992 sf0818491279 8 18493992 2.90E-08 1.75E-06
vg0721160145 sf0721159152 7 21160145 2.42E-07 3.53E-06
vg0921113209 sf0921112728 9 21113209 6.28E-07 4.38E-06
vg0921003290 sf0921002809 9 21003290 5.33E-06 NA
vg1122165203 sf1121699074 11 22165203 NA 1.79E-06