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 mr1848 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
vg0714475265 sf0714474272 7 14475265 1.82E-09 1.82E-09
vg0922282634 sf0922282153 9 22282634 2.37E-08 2.37E-08
vg0626920669 sf0626919672 6 26920669 3.14E-08 3.14E-08
vg1204328784 sf1204327772 12 4328784 6.01E-08 6.01E-08
vg0318856031 sf0318854791 3 18856031 1.04E-07 1.04E-07
vg0228241702 sf0228235833 2 28241702 1.36E-07 1.36E-07
vg0804836535 sf0804835538 8 4836535 2.13E-07 2.13E-07
vg0415473298 sf0415463981 4 15473298 3.95E-07 3.95E-07
vg0103858123 sf0103857123 1 3858123 9.42E-07 9.42E-07
vg0915839206 sf0915838205 9 15839206 1.02E-06 1.02E-06
vg0217256342 sf0217250472 2 17256342 1.08E-06 1.08E-06
vg1019533706 sf1019462230 10 19533706 1.25E-06 1.25E-06
vg0901839940 sf0901838940 9 1839940 2.04E-06 2.04E-06
vg1222407333 sf1222373772 12 22407333 2.88E-06 2.89E-06
vg0921230909 sf0921230428 9 21230909 2.90E-06 2.90E-06
vg0111639734 sf0111638708 1 11639734 2.91E-06 2.91E-06
vg0330235697 sf0330228736 3 30235697 3.08E-06 3.08E-06
vg0610634708 sf0610633709 6 10634708 3.66E-06 3.66E-06