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 mr1970 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
vg0611239376 sf0611238377 6 11239376 3.20E-07 3.20E-07
vg1122427075 sf1121960946 11 22427075 5.69E-07 5.69E-07
vg1209876216 sf1209873626 12 9876216 7.69E-07 7.69E-07
vg0600569739 sf0600568740 6 569739 1.71E-06 1.71E-06
vg0404978718 sf0404974157 4 4978718 2.24E-06 2.24E-06
vg0620820526 sf0620819529 6 20820526 2.56E-06 2.56E-06
vg1016814608 sf1016743380 10 16814608 2.65E-06 2.65E-06
vg0306899668 sf0306898666 3 6899668 4.43E-06 4.43E-06