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 mr1180 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
vg0910745892 sf0910744891 9 10745892 2.72E-13 NA
vg0528575652 sf0528513007 5 28575652 1.65E-11 NA
vg1204514412 sf1204513400 12 4514412 2.72E-11 NA
vg0726219340 sf0726218346 7 26219340 4.93E-11 NA
vg0813554256 sf0813551809 8 13554256 5.50E-11 NA
vg0806547817 sf0806546822 8 6547817 1.81E-09 3.69E-06
vg0724768412 sf0724767418 7 24768412 1.81E-08 NA
vg1204217058 sf1204216046 12 4217058 1.87E-08 NA
vg0721325215 sf0721324222 7 21325215 2.09E-07 NA
vg0708430086 sf0708429091 7 8430086 4.18E-07 2.18E-06
vg0205588537 sf0205588537 2 5588537 NA 4.47E-08
vg1120732145 sf1120266048 11 20732145 NA 2.37E-06