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 mr1507 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
vg1218087170 sf1218058606 12 18087170 3.57E-09 2.20E-06
vg0327979488 sf0327972542 3 27979488 3.55E-08 6.83E-06
vg0910450391 sf0910449390 9 10450391 4.35E-08 2.02E-06
vg0328102373 sf0328095427 3 28102373 4.46E-08 NA
vg1221127987 sf1221094537 12 21127987 9.60E-08 9.16E-06
vg0208677057 sf0208677056 2 8677057 2.63E-07 NA
vg0208596573 sf0208596572 2 8596573 8.05E-07 NA
vg0327981223 sf0327974277 3 27981223 8.30E-06 NA
vg1214006412 sf1214003752 12 14006412 NA 2.07E-06
vg1210657344 sf1210654757 12 10657344 NA 2.38E-06