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 mr1235 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
vg0216746978 sf0216741108 2 16746978 7.40E-87 2.04E-19
vg0719559025 sf0719558032 7 19559025 4.98E-60 NA
vg0205725551 sf0205725551 2 5725551 1.89E-58 NA
vg0128362507 sf0128361463 1 28362507 3.38E-58 NA
vg0140395579 sf0140394536 1 40395579 6.32E-57 NA
vg0216804396 sf0216798526 2 16804396 NA 4.86E-16
vg0217232931 sf0217227061 2 17232931 NA 8.12E-07
vg0402290555 sf0402286150 4 2290555 NA 1.92E-06
vg0608187836 sf0608186837 6 8187836 NA 2.19E-06
vg0216957396 sf0216951526 2 16957396 NA 3.08E-06
vg1124229055 sf1123762925 11 24229055 NA 4.78E-06
vg0216576140 sf0216570270 2 16576140 NA 4.87E-06