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 mr1497 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
vg1121250679 sf1120784557 11 21250679 9.91E-07 9.97E-07
vg1106628056 sf1106623809 11 6628056 1.15E-06 1.15E-06
vg1215172539 sf1215169875 12 15172539 1.21E-06 1.22E-06
vg1122503059 sf1122036930 11 22503059 3.02E-06 3.04E-06
vg0113419706 sf0113418680 1 13419706 3.61E-06 3.62E-06
vg0501509057 sf0501509041 5 1509057 3.83E-06 3.85E-06
vg0327981236 sf0327974290 3 27981236 4.04E-06 4.06E-06
vg0827341982 sf0827339268 8 27341982 4.11E-06 4.13E-06
vg0405832157 sf0405827596 4 5832157 4.52E-06 4.53E-06
vg0606734750 sf0606733751 6 6734750 4.62E-06 4.65E-06