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 mr1544 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
vg1122072549 sf1121606420 11 22072549 8.14E-09 NA
vg0104612596 sf0104611596 1 4612596 9.23E-08 NA
vg0827235441 sf0827232727 8 27235441 6.79E-07 NA
vg0827934606 sf0827931892 8 27934606 7.20E-07 8.69E-06
vg0221679698 sf0221673829 2 21679698 3.71E-06 NA
vg1122149845 sf1121683716 11 22149845 3.88E-06 6.17E-06
vg0910453386 sf0910452385 9 10453386 NA 1.41E-06
vg1209459428 sf1209456837 12 9459428 NA 1.42E-06
vg0504429178 sf0504429155 5 4429178 NA 5.54E-06