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 mr1217 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
vg0515177250 sf0515119792 5 15177250 1.41E-08 3.75E-06
vg1100538307 sf1100537310 11 538307 2.09E-08 5.40E-06
vg1108386798 sf1108381408 11 8386798 2.25E-08 5.78E-07
vg0326593742 sf0326586796 3 26593742 6.91E-08 7.86E-06
vg0319091716 sf0319090476 3 19091716 1.19E-07 3.05E-06
vg1003557200 sf1003556177 10 3557200 NA 2.55E-06