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 mr1366 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
vg0800226466 sf0800225466 8 226466 4.92E-07 4.93E-07
vg1123192315 sf1122726186 11 23192315 1.14E-06 1.14E-06
vg0132271441 sf0132270397 1 32271441 2.29E-06 2.29E-06
vg1219215446 sf1219186916 12 19215446 2.92E-06 2.92E-06
vg0800237681 sf0800236681 8 237681 2.96E-06 2.95E-06
vg1001246161 sf1001245138 10 1246161 4.65E-06 4.64E-06
vg0910846993 sf0910845992 9 10846993 4.88E-06 4.88E-06