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 mr1903 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
vg0524607520 sf0524544940 5 24607520 1.01E-58 4.03E-28
vg0524555608 sf0524493029 5 24555608 1.85E-58 5.72E-29
vg0524690035 sf0524627455 5 24690035 4.10E-31 5.21E-14
vg0502008041 sf0502008023 5 2008041 2.75E-30 NA
vg0604632189 sf0604631190 6 4632189 3.82E-30 NA
vg0114289141 sf0114288115 1 14289141 2.18E-28 NA
vg0112316430 sf0112315404 1 12316430 1.48E-25 NA
vg0524738001 sf0524675422 5 24738001 NA 1.68E-21
vg1100365076 sf1100364078 11 365076 NA 2.20E-08
vg0524106953 sf0524044372 5 24106953 NA 1.05E-07
vg0525086138 sf0525023553 5 25086138 NA 7.42E-07
vg0234925070 sf0234919201 2 34925070 NA 2.71E-06
vg0524381828 sf0524319249 5 24381828 NA 2.78E-06