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 mr1624 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
vg0710971660 sf0710970666 7 10971660 9.85E-12 NA
vg0618236227 sf0618235230 6 18236227 3.12E-11 NA
vg0722872422 sf0722871429 7 22872422 5.97E-10 NA
vg0714560467 sf0714559474 7 14560467 1.38E-09 NA
vg0919075740 sf0919075329 9 19075740 4.10E-09 NA
vg0712275750 sf0712274757 7 12275750 1.10E-07 NA
vg0414225343 sf0414216056 4 14225343 2.29E-07 NA
vg0605662134 sf0605661135 6 5662134 NA 1.89E-06
vg0803658896 sf0803657899 8 3658896 NA 3.36E-06
vg1003626827 sf1003625804 10 3626827 NA 4.63E-06