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 mr1269 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
vg0133316697 sf0133315653 1 33316697 1.40E-09 NA
vg0316612389 sf0316611034 3 16612389 3.90E-09 NA
vg0611452885 sf0611451886 6 11452885 7.34E-09 NA
vg0234397577 sf0234391708 2 34397577 9.74E-09 NA
vg0230066458 sf0230060589 2 30066458 2.50E-08 NA
vg0607694365 sf0607693366 6 7694365 4.70E-08 NA
vg0619397284 sf0619396287 6 19397284 4.72E-07 8.14E-06
vg0226834402 sf0226828533 2 26834402 1.48E-06 NA
vg0221393191 sf0221387323 2 21393191 NA 2.15E-06