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 mr1458 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
vg0425144906 sf0424959767 4 25144906 1.09E-08 3.50E-06
vg1218885208 sf1218856643 12 18885208 1.46E-08 NA
vg1218508238 sf1218479674 12 18508238 2.22E-08 7.86E-06
vg0418797097 sf0418625142 4 18797097 2.76E-08 NA
vg1011449672 sf1011378491 10 11449672 2.94E-08 4.72E-06
vg1218447354 sf1218418790 12 18447354 4.10E-07 1.51E-07
vg1218706273 sf1218677708 12 18706273 4.24E-07 1.42E-06
vg1122663951 sf1122197822 11 22663951 2.00E-06 NA
vg0809163559 sf0809162563 8 9163559 4.28E-06 NA