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 mr1041 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
vg1227173062 sf1227139462 12 27173062 2.42E-09 NA
vg0105521069 sf0105520069 1 5521069 1.23E-08 NA
vg1104987798 sf1104983609 11 4987798 1.70E-08 NA
vg1207873877 sf1207871283 12 7873877 2.60E-08 NA
vg0305129097 sf0305128099 3 5129097 3.05E-08 NA
vg1013275525 sf1013204295 10 13275525 8.12E-08 2.51E-06
vg0220342715 sf0220336847 2 20342715 1.04E-07 9.87E-06
vg0819439794 sf0819437081 8 19439794 1.16E-07 3.61E-06
vg0434768134 sf0434583025 4 34768134 1.77E-07 1.60E-07
vg1207840077 sf1207837483 12 7840077 3.06E-07 2.85E-06
vg0232481318 sf0232475449 2 32481318 2.26E-06 2.15E-07
vg0232446567 sf0232440698 2 32446567 NA 2.66E-06
vg1125669886 sf1125203725 11 25669886 NA 2.66E-06