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 mr1477 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
vg0616175231 sf0616174233 6 16175231 9.48E-36 5.83E-07
vg0612782029 sf0612781030 6 12782029 5.12E-35 2.41E-06
vg0620431139 sf0620430142 6 20431139 7.29E-34 1.89E-07
vg0620435111 sf0620434114 6 20435111 1.82E-33 1.92E-07
vg0611275662 sf0611274663 6 11275662 5.68E-33 2.91E-07
vg0127650549 sf0127649505 1 27650549 2.24E-32 NA
vg0307439017 sf0307437955 3 7439017 3.85E-32 NA
vg0610367772 sf0610366773 6 10367772 NA 4.17E-07
vg1209080302 sf1209077711 12 9080302 NA 1.68E-06
vg1004618983 sf1004635521 10 4618983 NA 3.35E-06