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 mr1318 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
vg0906631032 sf0906630032 9 6631032 1.17E-09 1.17E-07
vg0915815139 sf0915814138 9 15815139 1.37E-08 2.26E-07
vg1210647989 sf1210645402 12 10647989 2.26E-08 NA
vg1215167085 sf1215164421 12 15167085 9.97E-08 NA
vg0916030541 sf0916029540 9 16030541 3.45E-07 2.12E-07
vg1214134657 sf1214131997 12 14134657 8.22E-07 3.09E-06
vg1004573441 sf1004589979 10 4573441 2.43E-06 2.46E-06
vg0433421279 sf0433236168 4 33421279 NA 3.70E-07
vg1214656787 sf1214654127 12 14656787 NA 6.73E-07
vg0117840935 sf0117839889 1 17840935 NA 2.00E-06
vg0400387960 sf0400386958 4 387960 NA 2.16E-06
vg1004566535 sf1004583073 10 4566535 NA 3.15E-06