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 mr1689 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
vg1016393079 sf1016321855 10 16393079 3.34E-25 NA
vg1225011564 sf1224978018 12 25011564 1.54E-24 NA
vg0710020952 sf0710019958 7 10020952 2.75E-24 NA
vg0717175691 sf0717174698 7 17175691 2.78E-24 NA
vg0407849294 sf0407844562 4 7849294 6.93E-24 NA
vg0729550923 sf0729549931 7 29550923 1.11E-23 NA
vg0709859067 sf0709858073 7 9859067 9.68E-23 4.15E-06
vg1016762508 sf1016691281 10 16762508 1.03E-22 4.01E-06
vg1209679986 sf1209677395 12 9679986 NA 2.94E-07
vg0909036511 sf0909035510 9 9036511 NA 9.41E-07