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 mr1092 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
vg1109729286 sf1109723863 11 9729286 3.29E-09 1.92E-07
vg0911559557 sf0911558556 9 11559557 7.17E-09 NA
vg1119855883 sf1119389806 11 19855883 8.10E-09 NA
vg0910385915 sf0910384914 9 10385915 1.34E-08 NA
vg1217394893 sf1217388848 12 17394893 1.43E-08 NA
vg1115483994 sf1115020307 11 15483994 7.39E-08 3.54E-06
vg0723664033 sf0723663040 7 23664033 6.81E-07 NA
vg0800488569 sf0800487569 8 488569 8.42E-07 NA
vg1009516560 sf1009445381 10 9516560 1.38E-06 2.38E-06