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 mr1165 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
vg0610871475 sf0610870476 6 10871475 1.49E-22 1.05E-09
vg0610861074 sf0610860075 6 10861074 2.03E-22 6.94E-11
vg0618509091 sf0618508094 6 18509091 1.63E-19 NA
vg0205554214 sf0205554214 2 5554214 1.10E-18 NA
vg0524588276 sf0524525696 5 24588276 2.23E-18 NA
vg0615048049 sf0615047050 6 15048049 4.85E-18 NA
vg1020583266 sf1020511745 10 20583266 1.22E-16 NA
vg0502125341 sf0502125315 5 2125341 NA 9.37E-08
vg0518363321 sf0518302807 5 18363321 NA 1.22E-07
vg0727995401 sf0727994408 7 27995401 NA 2.79E-07
vg1004623296 sf1004639834 10 4623296 NA 9.08E-07
vg1004623685 sf1004640223 10 4623685 NA 9.09E-07
vg1101962366 sf1101961366 11 1962366 NA 1.65E-06
vg0608916603 sf0608915604 6 8916603 NA 2.08E-06
vg0612638166 sf0612637167 6 12638166 NA 2.80E-06
vg0608911819 sf0608910820 6 8911819 NA 4.15E-06
vg1207394291 sf1207391698 12 7394291 NA 5.45E-06