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 mr1807 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
vg0501240005 sf0501239989 5 1240005 5.99E-10 7.56E-07
vg0217511782 sf0217505912 2 17511782 1.24E-09 NA
vg0805565852 sf0805564855 8 5565852 1.70E-09 NA
vg0528845654 sf0528783009 5 28845654 2.31E-09 NA
vg0805178156 sf0805177159 8 5178156 4.34E-09 NA
vg0210599887 sf0210599885 2 10599887 1.07E-08 2.86E-06
vg1012018661 sf1011947476 10 12018661 6.31E-08 NA
vg1227054616 sf1227021015 12 27054616 2.32E-07 2.11E-06
vg0214794497 sf0214788627 2 14794497 1.27E-06 NA
vg1122793429 sf1122327300 11 22793429 4.02E-06 NA
vg0805695351 sf0805694354 8 5695351 6.33E-06 4.14E-06
vg0412166793 sf0412157504 4 12166793 NA 4.03E-06