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 mr1851 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
vg1022647600 sf1022576074 10 22647600 2.02E-08 NA
vg0306769175 sf0306768175 3 6769175 3.28E-08 NA
vg0728416802 sf0728415810 7 28416802 3.42E-08 NA
vg0220358695 sf0220352827 2 20358695 4.43E-08 NA
vg0223172450 sf0223166581 2 23172450 4.61E-08 NA
vg0605916372 sf0605915373 6 5916372 6.46E-08 4.75E-06
vg0901536604 sf0901535604 9 1536604 1.79E-07 6.23E-07
vg0805645286 sf0805644289 8 5645286 2.32E-07 NA
vg0220340205 sf0220334337 2 20340205 5.21E-06 NA