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 mr1077 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
vg0222718166 sf0222712297 2 22718166 1.05E-46 4.11E-24
vg0222719569 sf0222713700 2 22719569 4.57E-46 3.03E-24
vg0222857256 sf0222851387 2 22857256 1.31E-27 3.14E-08
vg0229586698 sf0229580829 2 29586698 2.00E-23 NA
vg0204877627 sf0204877624 2 4877627 2.20E-23 NA
vg0120402133 sf0120401088 1 20402133 2.63E-23 NA
vg0223089153 sf0223083284 2 23089153 4.18E-23 NA
vg0315261472 sf0315260119 3 15261472 4.66E-22 NA
vg0314948067 sf0314946714 3 14948067 1.38E-19 2.14E-06
vg0222725003 sf0222719134 2 22725003 NA 4.69E-10
vg0222817468 sf0222811599 2 22817468 NA 5.81E-10
vg0223740427 sf0223734558 2 23740427 NA 7.31E-09
vg1112909023 sf1112445344 11 12909023 NA 2.54E-06
vg0222624216 sf0222618347 2 22624216 NA 3.49E-06