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 mr1148 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
vg0222725881 sf0222720012 2 22725881 4.75E-25 6.62E-19
vg0222725905 sf0222720036 2 22725905 5.17E-25 3.30E-19
vg0222727216 sf0222721347 2 22727216 5.37E-25 4.25E-19
vg0224263868 sf0224257999 2 24263868 5.03E-10 NA
vg0224723224 sf0224717355 2 24723224 2.33E-09 4.72E-06
vg0229404686 sf0229398817 2 29404686 3.72E-09 NA
vg0223171967 sf0223166098 2 23171967 7.65E-09 3.22E-06
vg0221953494 sf0221947625 2 21953494 2.20E-08 4.87E-06
vg0224676560 sf0224670691 2 24676560 3.45E-07 1.96E-06
vg0222624829 sf0222618960 2 22624829 1.99E-06 1.16E-06
vg0710331865 sf0710330871 7 10331865 9.32E-06 2.39E-06