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 mr1846 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
vg1215077450 sf1215074791 12 15077450 4.57E-08 4.57E-08
vg0601659985 sf0601658986 6 1659985 4.61E-07 4.61E-07
vg0805959456 sf0805958459 8 5959456 6.12E-07 6.12E-07
vg0921699962 sf0921699481 9 21699962 1.18E-06 1.18E-06
vg1215669490 sf1215666787 12 15669490 1.41E-06 1.41E-06
vg0720474327 sf0720473334 7 20474327 2.45E-06 2.45E-06
vg0517668715 sf0517608356 5 17668715 2.59E-06 2.59E-06
vg0223171948 sf0223166079 2 23171948 3.53E-06 3.53E-06
vg1015661029 sf1015589799 10 15661029 3.74E-06 3.74E-06
vg0906912896 sf0906911896 9 6912896 4.45E-06 4.45E-06