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 mr1054 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
vg0414197719 sf0414188435 4 14197719 8.63E-09 NA
vg1001363211 sf1001362188 10 1363211 9.22E-09 5.27E-06
vg0225148969 sf0225143100 2 25148969 3.35E-08 NA
vg0315350100 sf0315348747 3 15350100 5.02E-08 NA
vg0818230180 sf0818227467 8 18230180 6.88E-08 NA
vg1117178010 sf1116711862 11 17178010 3.26E-07 NA
vg0909402515 sf0909401514 9 9402515 3.83E-07 NA
vg0406883539 sf0406878798 4 6883539 4.38E-06 3.27E-06
vg0406715803 sf0406711250 4 6715803 4.87E-06 1.49E-06
vg1002941120 sf1002940097 10 2941120 6.68E-06 1.72E-07
vg0103143509 sf0103142509 1 3143509 NA 1.69E-06
vg0715817404 sf0715816411 7 15817404 NA 3.76E-06
vg1001392057 sf1001391034 10 1392057 NA 4.94E-06