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 mr1359 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
vg1117720606 sf1117254462 11 17720606 1.19E-09 NA
vg0619610104 sf0619609107 6 19610104 1.87E-09 NA
vg0132222646 sf0132221602 1 32222646 1.93E-09 NA
vg1218289979 sf1218261415 12 18289979 6.58E-09 NA
vg0630306971 sf0630305973 6 30306971 1.12E-08 NA
vg0101289411 sf0101288411 1 1289411 1.35E-08 3.18E-06
vg0326156469 sf0326154488 3 26156469 1.70E-08 3.75E-06
vg0432038119 sf0431853012 4 32038119 1.83E-08 1.17E-06
vg0137351314 sf0137350271 1 37351314 1.86E-07 2.15E-06
vg0333204929 sf0333197799 3 33204929 7.11E-07 2.20E-06
vg0329851473 sf0329844512 3 29851473 3.66E-06 6.56E-06