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 mr1057 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
vg0105144997 sf0105143997 1 5144997 4.47E-21 3.02E-15
vg0906427214 sf0906426214 9 6427214 3.20E-09 1.96E-06
vg0207379019 sf0207379019 2 7379019 1.05E-08 NA
vg1212211715 sf1212209053 12 12211715 2.70E-08 NA
vg1220441290 sf1220412732 12 20441290 6.01E-08 NA
vg0207704215 sf0207704214 2 7704215 6.96E-08 2.32E-08
vg1213065934 sf1213063273 12 13065934 1.05E-07 5.89E-07
vg1215548475 sf1215545772 12 15548475 6.56E-07 NA
vg0106157133 sf0106156133 1 6157133 7.82E-07 2.36E-06
vg0404570369 sf0404565972 4 4570369 5.66E-06 NA
vg0727277278 sf0727276284 7 27277278 NA 1.73E-06