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 mr1592 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
vg0222719586 sf0222713717 2 22719586 3.14E-18 6.95E-14
vg0225032737 sf0225026868 2 25032737 4.92E-09 5.79E-06
vg1127678069 sf1127206456 11 27678069 1.12E-08 3.26E-06
vg0224274079 sf0224268210 2 24274079 2.00E-08 NA
vg1127790119 sf1127318505 11 27790119 3.03E-08 5.81E-06
vg0601478451 sf0601477452 6 1478451 5.37E-08 NA
vg0223007008 sf0223001139 2 23007008 9.54E-08 1.53E-06
vg1218127576 sf1218099012 12 18127576 NA 6.30E-07