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 mr1720 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
vg1204775308 sf1204774293 12 4775308 6.37E-18 9.63E-11
vg0420828431 sf0420656474 4 20828431 1.35E-15 8.92E-07
vg0520083803 sf0520021279 5 20083803 1.70E-15 NA
vg0529405800 sf0529343155 5 29405800 7.44E-15 NA
vg0138814689 sf0138813646 1 38814689 9.14E-14 NA
vg0909366654 sf0909365653 9 9366654 9.37E-14 8.73E-07
vg0141992653 sf0141991610 1 41992653 1.35E-12 NA
vg0134374494 sf0134373451 1 34374494 8.95E-12 1.04E-11
vg0432593833 sf0432408724 4 32593833 1.22E-11 3.26E-06
vg0827252347 sf0827249633 8 27252347 1.65E-11 1.28E-06
vg0132263132 sf0132262088 1 32263132 1.18E-10 1.97E-06
vg0432660385 sf0432475274 4 32660385 3.33E-10 2.43E-06
vg0134372447 sf0134371404 1 34372447 NA 9.54E-09
vg1204744101 sf1204743086 12 4744101 NA 1.90E-07
vg0519481936 sf0519419420 5 19481936 NA 4.39E-07
vg1016915671 sf1016844443 10 16915671 NA 5.15E-07
vg1218165628 sf1218137064 12 18165628 NA 1.10E-06
vg0620101204 sf0620100207 6 20101204 NA 1.33E-06
vg0817437807 sf0817435093 8 17437807 NA 2.42E-06
vg0133875165 sf0133874121 1 33875165 NA 2.51E-06
vg0404806507 sf0404801946 4 4806507 NA 3.18E-06
vg0140754215 sf0140753172 1 40754215 NA 3.43E-06