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 mr1511 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
vg1017098057 sf1017026829 10 17098057 1.05E-08 8.73E-08
vg0729692653 sf0729691661 7 29692653 1.14E-07 2.36E-07
vg1205533146 sf1205532132 12 5533146 1.30E-07 3.57E-06
vg0328933796 sf0328926848 3 28933796 3.39E-07 3.30E-06
vg1005148582 sf1005165119 10 5148582 4.41E-07 1.72E-07
vg0623833223 sf0623832226 6 23833223 5.43E-07 1.32E-06
vg1120972390 sf1120506269 11 20972390 1.45E-06 9.95E-06
vg1016458264 sf1016387037 10 16458264 2.29E-06 4.65E-06