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 mr1147 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
vg0714251445 sf0714250452 7 14251445 1.63E-08 2.54E-08
vg0412455905 sf0412446620 4 12455905 3.16E-08 1.42E-07
vg1121617620 sf1121151497 11 21617620 9.66E-08 6.88E-08
vg1006197978 sf1006213627 10 6197978 1.55E-07 2.46E-07
vg1009318270 sf1009247091 10 9318270 1.77E-07 1.66E-07
vg1009151297 sf1009080118 10 9151297 4.57E-07 7.15E-07
vg1117431373 sf1116965228 11 17431373 6.60E-07 5.60E-06
vg0714252091 sf0714251098 7 14252091 1.33E-06 1.26E-06
vg0719000915 sf0718999922 7 19000915 NA 8.66E-06