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 mr1363 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
vg0710257925 sf0710256931 7 10257925 7.77E-12 NA
vg0506005338 sf0506005277 5 6005338 2.43E-11 NA
vg0711119293 sf0711118299 7 11119293 3.80E-11 3.12E-06
vg0331745883 sf0331738760 3 31745883 1.09E-10 NA
vg0431203262 sf0431018152 4 31203262 1.79E-10 NA
vg1219459084 sf1219430554 12 19459084 1.95E-10 NA
vg0505471969 sf0505471947 5 5471969 2.80E-10 2.53E-06
vg0126640706 sf0126639662 1 26640706 7.32E-10 7.17E-07
vg0123461399 sf0123460355 1 23461399 1.55E-09 1.04E-07
vg0401608764 sf0401604313 4 1608764 2.91E-09 4.80E-06
vg1214701815 sf1214699156 12 14701815 9.77E-09 3.15E-06
vg1207511374 sf1207508780 12 7511374 5.25E-08 6.80E-08
vg0622289909 sf0622288912 6 22289909 2.17E-07 4.23E-06
vg0616722436 sf0616721438 6 16722436 2.84E-07 NA
vg1214347472 sf1214344812 12 14347472 6.13E-07 NA
vg0208170112 sf0208170111 2 8170112 1.04E-06 3.39E-06
vg0118245400 sf0118244354 1 18245400 NA 6.36E-07
vg0519441155 sf0519378639 5 19441155 NA 3.75E-06
vg0714390906 sf0714389913 7 14390906 NA 4.98E-06