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 mr1794 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
vg1110049605 sf1110044182 11 10049605 1.21E-09 2.85E-09
vg0910525504 sf0910524503 9 10525504 1.74E-09 NA
vg0607152342 sf0607151343 6 7152342 3.95E-09 NA
vg0119116783 sf0119115738 1 19116783 7.34E-09 NA
vg0910780392 sf0910779391 9 10780392 7.53E-09 NA
vg0520984197 sf0520921638 5 20984197 1.76E-08 3.98E-08
vg1125224256 sf1124758096 11 25224256 3.28E-08 1.15E-07
vg1008951584 sf1008880445 10 8951584 8.87E-08 2.87E-06
vg0307478433 sf0307477371 3 7478433 1.09E-07 3.43E-06
vg1019348557 sf1019277112 10 19348557 1.17E-07 2.18E-06
vg1224302733 sf1224269186 12 24302733 1.48E-07 9.19E-07
vg0227743836 sf0227737967 2 27743836 2.10E-07 1.11E-06
vg0529701170 sf0529638525 5 29701170 3.70E-07 6.72E-07
vg0826832590 sf0826829876 8 26832590 1.31E-06 1.53E-06
vg0113433238 sf0113432212 1 13433238 2.13E-06 NA
vg0403844302 sf0403839906 4 3844302 NA 1.02E-06
vg0137534290 sf0137533247 1 37534290 NA 2.76E-06