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 mr1372 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
vg1117484883 sf1117018738 11 17484883 4.54E-09 1.43E-06
vg1001363211 sf1001362188 10 1363211 6.25E-09 4.65E-06
vg0312560454 sf0312559172 3 12560454 5.14E-08 NA
vg0414197719 sf0414188435 4 14197719 5.21E-08 NA
vg0315350100 sf0315348747 3 15350100 6.73E-08 NA
vg1107619278 sf1107615023 11 7619278 2.83E-06 NA
vg0406883539 sf0406878798 4 6883539 3.72E-06 4.03E-06
vg0103143509 sf0103142509 1 3143509 NA 1.05E-06
vg1002941120 sf1002940097 10 2941120 NA 1.07E-06
vg1105433765 sf1105429516 11 5433765 NA 3.24E-06
vg0406864460 sf0406859905 4 6864460 NA 3.38E-06