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 mr1032 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
vg0727995401 sf0727994408 7 27995401 2.02E-10 NA
vg1100066353 sf1100065353 11 66353 8.23E-10 NA
vg1217636564 sf1217630519 12 17636564 3.55E-09 NA
vg0138112582 sf0138111539 1 38112582 4.02E-09 NA
vg0130089725 sf0130088680 1 30089725 5.02E-09 NA
vg0419746635 sf0419574670 4 19746635 7.46E-08 4.58E-06
vg0614958335 sf0614957336 6 14958335 1.57E-07 NA
vg0502125341 sf0502125315 5 2125341 2.37E-07 8.40E-08
vg1121160624 sf1120694503 11 21160624 5.32E-06 NA
vg0524166710 sf0524104129 5 24166710 9.86E-06 NA