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 mr1649 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
vg0325710457 sf0325708475 3 25710457 3.72E-08 3.72E-08
vg1206482579 sf1206481469 12 6482579 6.50E-07 6.50E-07
vg0705490216 sf0705489217 7 5490216 1.13E-06 1.13E-06
vg1020402458 sf1020330938 10 20402458 1.33E-06 1.33E-06
vg1005136400 sf1005152937 10 5136400 1.99E-06 1.99E-06
vg0323669384 sf0323667558 3 23669384 2.26E-06 2.26E-06
vg0202722002 sf0202722000 2 2722002 2.95E-06 2.95E-06
vg1004753931 sf1004770468 10 4753931 3.59E-06 3.59E-06
vg0221849531 sf0221843662 2 21849531 4.10E-06 4.10E-06
vg0703703405 sf0703702406 7 3703405 4.75E-06 4.75E-06