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 mr1853 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
vg0921571697 sf0921571216 9 21571697 1.03E-08 NA
vg0315319561 sf0315318208 3 15319561 1.42E-08 NA
vg1019944411 sf1019872911 10 19944411 3.00E-08 9.23E-06
vg0727516818 sf0727515824 7 27516818 3.06E-08 2.32E-06
vg1224751514 sf1224717968 12 24751514 5.11E-08 NA
vg0904766722 sf0904765722 9 4766722 2.08E-07 6.85E-06