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 mr1629 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
vg0228295621 sf0228289752 2 28295621 9.83E-89 3.42E-11
vg0206752992 sf0206752992 2 6752992 1.86E-84 NA
vg0232113837 sf0232107968 2 32113837 1.21E-82 NA
vg0334632285 sf0334625155 3 34632285 8.64E-82 NA
vg0225506288 sf0225500419 2 25506288 1.51E-81 1.33E-06
vg0225551985 sf0225546116 2 25551985 2.21E-81 2.86E-07
vg0715404922 sf0715403929 7 15404922 2.93E-77 3.41E-08
vg0614107939 sf0614106940 6 14107939 1.18E-75 5.50E-07
vg1106481576 sf1106477328 11 6481576 NA 2.39E-06
vg0228138855 sf0228132986 2 28138855 NA 3.01E-06
vg0722665343 sf0722664350 7 22665343 NA 3.16E-06
vg1121943688 sf1121477559 11 21943688 NA 4.80E-06
vg1121947030 sf1121480901 11 21947030 NA 5.48E-06