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 mr1584 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
vg1019763130 sf1019691630 10 19763130 1.21E-32 NA
vg1216986107 sf1216980061 12 16986107 1.48E-32 NA
vg0310319070 sf0310317986 3 10319070 1.69E-32 NA
vg1214799703 sf1214797044 12 14799703 2.24E-31 1.92E-06
vg0315146805 sf0315145452 3 15146805 2.82E-31 NA
vg0805964617 sf0805963620 8 5964617 1.19E-30 NA
vg0815543792 sf0815541078 8 15543792 1.18E-27 NA
vg1209531524 sf1209528933 12 9531524 NA 2.68E-07
vg0905282574 sf0905281574 9 5282574 NA 5.30E-07
vg0413765723 sf0413756437 4 13765723 NA 1.10E-06
vg1215481439 sf1215478736 12 15481439 NA 1.24E-06
vg1206477744 sf1206476634 12 6477744 NA 1.27E-06
vg0127888161 sf0127887117 1 27888161 NA 1.98E-06
vg0717726967 sf0717725974 7 17726967 NA 3.40E-06
vg0411353933 sf0411344636 4 11353933 NA 4.73E-06
vg0413764976 sf0413755690 4 13764976 NA 6.33E-06