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 mr1838 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
vg0205292054 sf0205292052 2 5292054 6.72E-13 8.38E-08
vg0726964336 sf0726963342 7 26964336 8.38E-13 1.20E-06
vg0726847020 sf0726846026 7 26847020 6.11E-12 4.31E-07
vg0125460828 sf0125459784 1 25460828 1.31E-11 NA
vg0123684776 sf0123683732 1 23684776 7.89E-11 NA
vg0134968245 sf0134967202 1 34968245 8.88E-11 NA
vg0819602446 sf0819599733 8 19602446 8.36E-10 4.40E-07
vg1118367684 sf1117901542 11 18367684 7.29E-09 6.61E-06
vg0819679743 sf0819677030 8 19679743 1.07E-08 1.55E-07
vg0819561125 sf0819558412 8 19561125 2.71E-06 2.30E-06
vg0431655631 sf0431470524 4 31655631 4.73E-06 3.59E-06
vg0807847137 sf0807846141 8 7847137 NA 6.53E-06