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 mr1749 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
vg0719897669 sf0719896676 7 19897669 1.41E-12 7.14E-07
vg0316491917 sf0316490562 3 16491917 2.51E-11 NA
vg0141707795 sf0141706752 1 41707795 1.28E-10 NA
vg0217282044 sf0217276174 2 17282044 1.59E-10 8.51E-06
vg0306324536 sf0306323536 3 6324536 2.20E-10 NA
vg0620866647 sf0620865650 6 20866647 3.18E-10 2.95E-06
vg0142009982 sf0142008939 1 42009982 4.10E-10 4.17E-06
vg0620772181 sf0620771184 6 20772181 6.29E-10 1.50E-06
vg0417772638 sf0417600675 4 17772638 7.93E-09 NA
vg0525530135 sf0525467556 5 25530135 2.21E-08 1.40E-06
vg0529163752 sf0529101107 5 29163752 2.42E-08 4.32E-06
vg0417712235 sf0417540273 4 17712235 2.63E-07 4.42E-06
vg0620807173 sf0620806176 6 20807173 NA 4.12E-06