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 mr1533 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
vg1013489724 sf1013418494 10 13489724 7.41E-24 5.06E-15
vg1013513655 sf1013442425 10 13513655 4.59E-22 3.11E-13
vg0418051899 sf0417879940 4 18051899 2.13E-13 NA
vg0904643511 sf0904642511 9 4643511 5.16E-13 3.67E-06
vg1217552443 sf1217546398 12 17552443 9.98E-13 NA
vg0826362828 sf0826360114 8 26362828 4.18E-12 NA
vg1217551932 sf1217545887 12 17551932 5.51E-09 4.79E-06
vg1013452368 sf1013381138 10 13452368 NA 2.17E-07
vg1013161872 sf1013090643 10 13161872 NA 1.99E-06