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 mr1900 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
vg1125118463 sf1124652303 11 25118463 2.97E-24 1.26E-25
vg1125131895 sf1124665735 11 25131895 1.99E-12 2.85E-12
vg1125050424 sf1124584264 11 25050424 3.44E-11 1.88E-08
vg0415146457 sf0415137171 4 15146457 1.18E-08 NA
vg0704638640 sf0704637641 7 4638640 7.18E-08 NA
vg1128817982 sf1128294761 11 28817982 9.31E-08 2.83E-06
vg1124826416 sf1124360256 11 24826416 1.88E-07 1.64E-07
vg1125082418 sf1124616258 11 25082418 1.91E-07 3.06E-13
vg0224273930 sf0224268061 2 24273930 3.04E-07 3.24E-07
vg0619153237 sf0619152240 6 19153237 1.18E-06 NA
vg1125485978 sf1125019817 11 25485978 NA 1.68E-06