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 mr1877 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
vg0610587852 sf0610586853 6 10587852 2.01E-48 4.22E-17
vg0610564319 sf0610563320 6 10564319 5.53E-44 3.98E-17
vg0610480667 sf0610479668 6 10480667 2.92E-43 1.47E-15
vg0615389358 sf0615388359 6 15389358 6.89E-36 8.06E-07
vg0617303575 sf0617302578 6 17303575 3.44E-35 4.68E-08
vg0619163386 sf0619162389 6 19163386 3.37E-31 2.21E-06
vg0614799711 sf0614798712 6 14799711 1.36E-30 1.94E-06
vg0622249528 sf0622248531 6 22249528 6.78E-29 NA
vg0115227579 sf0115226553 1 15227579 7.79E-27 NA
vg0629122299 sf0629121301 6 29122299 1.71E-26 4.11E-06
vg0619863366 sf0619862369 6 19863366 3.82E-26 4.55E-07
vg0610860716 sf0610859717 6 10860716 7.75E-25 1.03E-06
vg0222739831 sf0222733962 2 22739831 NA 3.36E-20
vg0222716046 sf0222710177 2 22716046 NA 5.80E-11
vg0222573327 sf0222567458 2 22573327 NA 9.72E-09
vg0805901176 sf0805900179 8 5901176 NA 2.75E-08
vg0610787522 sf0610786523 6 10787522 NA 3.50E-08
vg1107384719 sf1107380464 11 7384719 NA 7.65E-08
vg0710034123 sf0710033129 7 10034123 NA 1.56E-07
vg0222656032 sf0222650163 2 22656032 NA 2.64E-07
vg0206177063 sf0206177063 2 6177063 NA 5.97E-07
vg0206177435 sf0206177435 2 6177435 NA 2.44E-06
vg0729298014 sf0729297022 7 29298014 NA 3.07E-06
vg0612211443 sf0612210444 6 12211443 NA 3.15E-06
vg0312184655 sf0312183373 3 12184655 NA 3.75E-06
vg0421627867 sf0421455917 4 21627867 NA 3.85E-06
vg1114063604 sf1113599925 11 14063604 NA 4.71E-06
vg0527033218 sf0526970574 5 27033218 NA 4.73E-06