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 mr1223 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
vg0620812986 sf0620811989 6 20812986 3.26E-32 1.10E-06
vg1013642262 sf1013571031 10 13642262 2.33E-31 NA
vg0217672570 sf0217666700 2 17672570 2.55E-30 8.43E-06
vg0613146169 sf0613145170 6 13146169 7.24E-30 NA
vg0625994310 sf0625993313 6 25994310 8.87E-30 NA
vg0819251922 sf0819249209 8 19251922 8.68E-29 8.56E-07
vg1215551588 sf1215548885 12 15551588 NA 1.95E-06
vg0206305166 sf0206305166 2 6305166 NA 2.46E-06
vg0529122099 sf0529059454 5 29122099 NA 3.20E-06