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 mr1084 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
vg0722226606 sf0722225613 7 22226606 1.41E-12 1.13E-06
vg0230082625 sf0230076756 2 30082625 1.73E-12 NA
vg1219850678 sf1219822148 12 19850678 5.20E-12 NA
vg0914990285 sf0914989284 9 14990285 1.51E-11 NA
vg0140420434 sf0140419391 1 40420434 1.92E-11 NA
vg0916030541 sf0916029540 9 16030541 2.35E-11 1.44E-06
vg0410044585 sf0410035282 4 10044585 2.40E-10 9.59E-07
vg0808100775 sf0808099779 8 8100775 5.34E-09 NA
vg0613133382 sf0613132383 6 13133382 7.25E-09 3.84E-06
vg0906503065 sf0906502065 9 6503065 NA 1.54E-06
vg0401720392 sf0401715941 4 1720392 NA 3.16E-06
vg0223518939 sf0223513070 2 23518939 NA 4.01E-06
vg1214822308 sf1214819649 12 14822308 NA 9.33E-06