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 mr1545 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
vg0129377963 sf0129376918 1 29377963 3.44E-09 1.45E-06
vg1210731615 sf1210729028 12 10731615 2.81E-08 NA
vg1121998197 sf1121532068 11 21998197 6.93E-08 5.62E-06
vg1121816831 sf1121350708 11 21816831 1.14E-06 6.02E-07
vg0124002704 sf0124001660 1 24002704 1.68E-06 NA
vg0331744233 sf0331737110 3 31744233 2.72E-06 9.37E-06
vg1210690673 sf1210688086 12 10690673 9.15E-06 4.42E-06
vg0514669939 sf0514612482 5 14669939 NA 3.30E-06
vg0514712143 sf0514654686 5 14712143 NA 3.75E-06