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 mr1308 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
vg0313147221 sf0313145939 3 13147221 1.35E-11 1.66E-06
vg1019775422 sf1019703922 10 19775422 2.11E-10 NA
vg0728265516 sf0728264524 7 28265516 3.42E-10 NA
vg0310341198 sf0310340114 3 10341198 7.28E-10 NA
vg0921571697 sf0921571216 9 21571697 9.68E-10 NA
vg0920272507 sf0920272026 9 20272507 8.60E-09 2.05E-06
vg0815916978 sf0815914264 8 15916978 5.38E-07 6.74E-06