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 mr1868 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
vg0222724011 sf0222718142 2 22724011 3.17E-59 9.82E-37
vg0525141137 sf0525078558 5 25141137 1.08E-34 NA
vg0906971590 sf0906970590 9 6971590 5.43E-34 NA
vg0500664660 sf0500664660 5 664660 7.97E-33 NA
vg0702447377 sf0702446378 7 2447377 9.64E-33 NA
vg0222693356 sf0222687487 2 22693356 2.53E-26 2.39E-07
vg0222741692 sf0222735823 2 22741692 1.06E-25 4.98E-17
vg0222567385 sf0222561516 2 22567385 NA 5.40E-15
vg0224832469 sf0224826600 2 24832469 NA 9.91E-09
vg0222729853 sf0222723984 2 22729853 NA 1.87E-08
vg0224019660 sf0224013791 2 24019660 NA 2.04E-07
vg0222847562 sf0222841693 2 22847562 NA 2.39E-07
vg0610463015 sf0610462016 6 10463015 NA 3.37E-07
vg0223638265 sf0223632396 2 23638265 NA 4.48E-07
vg0222799084 sf0222793215 2 22799084 NA 1.84E-06
vg0525239875 sf0525177296 5 25239875 NA 2.15E-06
vg0224293593 sf0224287724 2 24293593 NA 2.16E-06
vg0222730936 sf0222725067 2 22730936 NA 2.26E-06
vg0220759001 sf0220753133 2 20759001 NA 2.38E-06
vg0224821353 sf0224815484 2 24821353 NA 3.10E-06
vg0224856480 sf0224850611 2 24856480 NA 3.77E-06
vg0724693961 sf0724692967 7 24693961 NA 3.89E-06
vg1012841072 sf1012769887 10 12841072 NA 4.37E-06
vg0224820512 sf0224814643 2 24820512 NA 4.45E-06