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 mr1333 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
vg0914770963 sf0914769962 9 14770963 1.04E-36 6.20E-06
vg0914770988 sf0914769987 9 14770988 1.94E-36 3.17E-06
vg0917625536 sf0917624535 9 17625536 2.75E-36 NA
vg0922486580 sf0922486099 9 22486580 3.52E-36 NA
vg0504766271 sf0504766248 5 4766271 3.03E-35 NA
vg0626189169 sf0626188172 6 26189169 2.97E-34 NA
vg0201664747 sf0201664747 2 1664747 NA 1.65E-09
vg1016933579 sf1016862351 10 16933579 NA 1.86E-07
vg0625839941 sf0625838944 6 25839941 NA 1.42E-06
vg0412923857 sf0412914567 4 12923857 NA 1.48E-06
vg0319912427 sf0319910938 3 19912427 NA 1.67E-06
vg0602224473 sf0602223474 6 2224473 NA 3.01E-06
vg0709640174 sf0709639180 7 9640174 NA 3.15E-06
vg1214644369 sf1214641709 12 14644369 NA 3.82E-06
vg0317255027 sf0317253837 3 17255027 NA 4.35E-06
vg1003636372 sf1003635349 10 3636372 NA 4.86E-06