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 mr1747 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
vg0918774898 sf0918773898 9 18774898 1.63E-06 1.63E-06
vg0222002131 sf0221996262 2 22002131 2.89E-06 2.89E-06
vg1124179099 sf1123712969 11 24179099 3.66E-06 3.66E-06
vg0207698155 sf0207698154 2 7698155 3.98E-06 3.98E-06
vg0223583301 sf0223577432 2 23583301 3.99E-06 3.99E-06