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 mr1299 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
vg0400075143 sf0400074143 4 75143 1.37E-14 3.34E-06
vg1128511351 sf1127988130 11 28511351 1.10E-13 2.73E-08
vg0520272415 sf0520209888 5 20272415 4.77E-13 NA
vg0114353405 sf0114352379 1 14353405 2.47E-12 NA
vg0704257453 sf0704256454 7 4257453 2.85E-12 NA
vg1127963105 sf1127491491 11 27963105 2.03E-10 3.80E-06
vg1127488862 sf1127017249 11 27488862 6.58E-10 NA
vg1127497936 sf1127026323 11 27497936 8.24E-10 4.10E-06
vg1218087228 sf1218058664 12 18087228 NA 1.79E-06
vg1016884447 sf1016813219 10 16884447 NA 3.41E-06