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 mr1540 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
vg1125509643 sf1125043482 11 25509643 6.86E-09 6.86E-09
vg0713262354 sf0713261361 7 13262354 2.47E-08 2.47E-08
vg1214618940 sf1214616280 12 14618940 5.00E-08 5.00E-08
vg1214707367 sf1214704708 12 14707367 2.15E-07 2.15E-07
vg0104008756 sf0104007756 1 4008756 4.39E-07 4.39E-07
vg1200849729 sf1200848729 12 849729 6.95E-07 6.95E-07
vg1217808832 sf1217780266 12 17808832 7.41E-07 7.41E-07
vg1200183647 sf1200182647 12 183647 1.19E-06 1.20E-06
vg0713262986 sf0713261993 7 13262986 1.21E-06 1.21E-06
vg1102086445 sf1102082303 11 2086445 1.26E-06 1.26E-06
vg1005112746 sf1005129283 10 5112746 1.51E-06 1.51E-06
vg1126208526 sf1125736940 11 26208526 1.81E-06 1.81E-06
vg0818236084 sf0818233371 8 18236084 1.96E-06 1.96E-06
vg0320738098 sf0320736608 3 20738098 2.62E-06 2.62E-06
vg1108636902 sf1108631512 11 8636902 3.29E-06 3.29E-06