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 mr1175 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
vg0723991314 sf0723990320 7 23991314 7.49E-08 7.49E-08
vg0723923647 sf0723922653 7 23923647 9.41E-08 9.41E-08
vg0403589171 sf0403584772 4 3589171 2.82E-07 2.82E-07
vg0404034503 sf0404030110 4 4034503 2.65E-06 2.65E-06
vg0814635395 sf0814632681 8 14635395 2.81E-06 2.81E-06
vg0722461595 sf0722460602 7 22461595 3.39E-06 3.40E-06