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 mr1529 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
vg0720364932 sf0720363939 7 20364932 1.80E-07 1.80E-07
vg1207539985 sf1207537391 12 7539985 2.89E-07 2.89E-07
vg1216759594 sf1216753548 12 16759594 3.82E-07 3.82E-07
vg1208705079 sf1208702486 12 8705079 5.21E-07 5.21E-07
vg1211698356 sf1211695692 12 11698356 5.87E-07 5.87E-07
vg0606957055 sf0606956056 6 6957055 9.93E-07 9.93E-07
vg0714470576 sf0714469583 7 14470576 1.39E-06 1.39E-06
vg1214669115 sf1214666455 12 14669115 1.87E-06 1.87E-06
vg1207387105 sf1207384512 12 7387105 2.49E-06 2.49E-06
vg1215178307 sf1215175643 12 15178307 3.77E-06 3.77E-06
vg0401440485 sf0401436035 4 1440485 3.99E-06 3.99E-06
vg0302837094 sf0302836090 3 2837094 4.29E-06 4.29E-06
vg1217803999 sf1217775433 12 17803999 4.64E-06 4.64E-06
vg0401505122 sf0401500672 4 1505122 4.91E-06 4.91E-06
vg0330231538 sf0330224577 3 30231538 7.78E-06 7.78E-06
vg1220174255 sf1220145697 12 20174255 9.03E-06 9.03E-06