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 mr1579 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
vg0208736544 sf0208736543 2 8736544 1.55E-18 8.13E-07
vg0208744094 sf0208744093 2 8744094 1.93E-18 7.39E-07
vg1226193413 sf1226159807 12 26193413 1.70E-16 NA
vg0907750359 sf0907749359 9 7750359 5.99E-16 NA
vg0308428130 sf0308427068 3 8428130 2.38E-15 NA
vg0313617458 sf0313616175 3 13617458 3.01E-15 4.06E-06
vg0907746354 sf0907745354 9 7746354 9.86E-15 NA
vg0523087948 sf0523025389 5 23087948 2.68E-13 NA
vg0229949816 sf0229943947 2 29949816 7.25E-13 NA
vg0208707423 sf0208707422 2 8707423 NA 2.37E-07
vg1122942578 sf1122476449 11 22942578 NA 2.01E-06
vg0222221610 sf0222215741 2 22221610 NA 2.16E-06
vg1215437580 sf1215434878 12 15437580 NA 2.36E-06