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 mr1531 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
vg0507041473 sf0507041415 5 7041473 1.75E-15 1.82E-10
vg0507044489 sf0507044431 5 7044489 6.09E-15 1.86E-10
vg0429738953 sf0429553823 4 29738953 1.38E-09 4.43E-06
vg1217950737 sf1217922172 12 17950737 3.09E-09 NA
vg0329590543 sf0329583583 3 29590543 5.40E-09 NA
vg0100779931 sf0100778931 1 779931 5.48E-09 NA
vg0428848253 sf0428663108 4 28848253 5.45E-08 NA
vg0133435988 sf0133434944 1 33435988 1.63E-06 4.72E-07
vg0133435968 sf0133434924 1 33435968 NA 6.93E-06