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 mr1852 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
vg0818614245 sf0818611532 8 18614245 3.60E-11 5.91E-07
vg0818666272 sf0818663559 8 18666272 1.14E-10 3.94E-07
vg0317880579 sf0317879361 3 17880579 1.45E-10 1.70E-07
vg0310496278 sf0310495194 3 10496278 1.43E-09 NA
vg0320620607 sf0320619117 3 20620607 2.30E-09 2.62E-07
vg0316484534 sf0316483179 3 16484534 4.03E-09 NA
vg0423794940 sf0423609797 4 23794940 4.75E-09 1.95E-06
vg0104411747 sf0104410747 1 4411747 5.07E-08 1.03E-06
vg0601621892 sf0601620893 6 1621892 5.60E-07 1.16E-06
vg0402546655 sf0402542258 4 2546655 7.28E-07 3.61E-06
vg0315983070 sf0315981717 3 15983070 2.84E-06 3.23E-07
vg0818186823 sf0818184110 8 18186823 3.26E-06 2.35E-06
vg1016877035 sf1016805807 10 16877035 8.63E-06 4.82E-06
vg0819496937 sf0819494224 8 19496937 NA 6.45E-08
vg0819478073 sf0819475360 8 19478073 NA 6.76E-08
vg0104428821 sf0104427821 1 4428821 NA 9.46E-07
vg0817298678 sf0817295964 8 17298678 NA 1.34E-06
vg0818172489 sf0818169776 8 18172489 NA 1.63E-06