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 mr1177 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
vg0404903044 sf0404898483 4 4903044 1.41E-08 5.95E-08
vg0629600778 sf0629599780 6 29600778 1.81E-08 5.56E-06
vg1224510581 sf1224477035 12 24510581 3.13E-08 2.30E-06
vg0432212227 sf0432027119 4 32212227 3.75E-08 5.08E-06
vg1209462715 sf1209460124 12 9462715 8.73E-08 4.28E-06
vg0421211457 sf0421039509 4 21211457 3.95E-07 1.37E-06
vg1001423491 sf1001422468 10 1423491 8.22E-06 NA
vg1206433093 sf1206431983 12 6433093 NA 4.54E-06