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 mr1418 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
vg0915815139 sf0915814138 9 15815139 2.80E-11 4.43E-07
vg0140420434 sf0140419391 1 40420434 8.72E-11 NA
vg0335297514 sf0335290383 3 35297514 1.05E-10 1.06E-06
vg0724945438 sf0724944444 7 24945438 1.20E-10 2.68E-06
vg0230082625 sf0230076756 2 30082625 1.67E-10 NA
vg0902107236 sf0902106236 9 2107236 2.05E-10 1.11E-06
vg0223521807 sf0223515938 2 23521807 2.11E-10 2.09E-06
vg1109865508 sf1109860085 11 9865508 1.98E-08 NA