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 mr1649 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
vg0335000939 sf0334993809 3 35000939 1.03E-14 8.27E-11
vg0216621262 sf0216615392 2 16621262 7.44E-14 2.85E-07
vg0216741216 sf0216735346 2 16741216 2.25E-13 6.78E-08
vg1008709315 sf1008638177 10 8709315 2.34E-13 NA
vg0216896614 sf0216890744 2 16896614 3.04E-13 7.93E-08
vg1005431305 sf1005447842 10 5431305 3.95E-13 NA
vg0334732696 sf0334725566 3 34732696 5.56E-13 4.85E-08
vg0402413441 sf0402409036 4 2413441 5.20E-12 NA
vg0908699614 sf0908698613 9 8699614 2.39E-10 NA
vg0216963088 sf0216957218 2 16963088 NA 8.16E-08
vg0327526492 sf0327519545 3 27526492 NA 5.08E-07
vg0327427154 sf0327420207 3 27427154 NA 6.55E-06