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 mr1244 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
vg0610566237 sf0610565238 6 10566237 7.01E-27 4.36E-13
vg0610472241 sf0610471242 6 10472241 1.02E-26 2.39E-14
vg0920309356 sf0920308875 9 20309356 5.49E-16 1.85E-08
vg0920309427 sf0920308946 9 20309427 6.51E-16 4.54E-09
vg0610802461 sf0610801462 6 10802461 1.02E-14 6.78E-06
vg0610803295 sf0610802296 6 10803295 1.17E-14 1.46E-06
vg0123815812 sf0123814768 1 23815812 3.34E-13 NA
vg0719259692 sf0719258699 7 19259692 4.17E-13 NA
vg0705277362 sf0705276363 7 5277362 6.19E-13 1.24E-06
vg0610401184 sf0610400185 6 10401184 2.83E-12 7.23E-07
vg0610875486 sf0610874487 6 10875486 8.31E-11 2.56E-06
vg0611950251 sf0611949252 6 11950251 2.68E-10 2.32E-06
vg0130523627 sf0130522583 1 30523627 3.05E-08 NA
vg0520363169 sf0520300642 5 20363169 NA 4.34E-07
vg0610752667 sf0610751668 6 10752667 NA 4.12E-06
vg0412792771 sf0412783481 4 12792771 NA 6.79E-06