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 mr1967 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
vg0709984451 sf0709983457 7 9984451 5.67E-08 5.68E-08
vg1215171621 sf1215168957 12 15171621 2.92E-07 2.92E-07
vg0303350062 sf0303349058 3 3350062 3.20E-07 3.20E-07
vg1214600105 sf1214597445 12 14600105 6.46E-07 6.46E-07
vg0710369624 sf0710368630 7 10369624 1.31E-06 1.31E-06
vg1210173449 sf1210170860 12 10173449 1.35E-06 1.35E-06
vg0820968372 sf0820965659 8 20968372 1.41E-06 1.41E-06
vg0710362096 sf0710361102 7 10362096 1.64E-06 1.64E-06
vg0723711493 sf0723710500 7 23711493 2.25E-06 2.25E-06
vg0431472905 sf0431287803 4 31472905 2.44E-06 2.44E-06
vg0710610393 sf0710609399 7 10610393 2.79E-06 2.79E-06
vg0431498650 sf0431313549 4 31498650 3.32E-06 3.32E-06
vg0200528076 sf0200528076 2 528076 3.64E-06 3.64E-06
vg1210723477 sf1210720890 12 10723477 3.73E-06 3.73E-06
vg0627961756 sf0627960758 6 27961756 4.02E-06 4.02E-06