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 mr1427 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
vg1128511488 sf1127988267 11 28511488 2.94E-11 9.66E-09
vg1128648694 sf1128125473 11 28648694 4.30E-11 1.44E-08
vg0315179799 sf0315178446 3 15179799 1.44E-10 9.01E-06
vg0315042815 sf0315041462 3 15042815 1.53E-10 2.09E-06
vg0316454459 sf0316453104 3 16454459 2.23E-09 NA
vg0420146692 sf0419974732 4 20146692 5.94E-09 NA
vg0818577556 sf0818574843 8 18577556 6.75E-09 5.82E-06
vg0432025550 sf0431840443 4 32025550 4.63E-07 NA
vg0327944341 sf0327937395 3 27944341 3.00E-06 NA
vg1218237165 sf1218208601 12 18237165 NA 5.81E-08
vg1016659254 sf1016588027 10 16659254 NA 2.63E-07
vg1218072048 sf1218043484 12 18072048 NA 3.78E-07
vg1119493431 sf1119027119 11 19493431 NA 1.66E-06
vg1114911197 sf1114447511 11 14911197 NA 1.68E-06
vg0910768444 sf0910767443 9 10768444 NA 9.16E-06