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 mr1973 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
vg0607383997 sf0607382998 6 7383997 9.77E-35 6.31E-17
vg0429319504 sf0429134370 4 29319504 3.56E-15 NA
vg0431722853 sf0431537745 4 31722853 5.08E-12 NA
vg0805703765 sf0805702768 8 5703765 7.48E-12 NA
vg0724768460 sf0724767466 7 24768460 1.14E-11 NA
vg0327582306 sf0327575359 3 27582306 2.27E-11 1.91E-06
vg0607240987 sf0607239988 6 7240987 3.15E-11 1.55E-06
vg0606974869 sf0606973870 6 6974869 4.67E-11 1.82E-07
vg1201578984 sf1201577984 12 1578984 6.25E-11 4.41E-07
vg0334583436 sf0334576306 3 34583436 1.51E-10 1.68E-06
vg1121249384 sf1120783262 11 21249384 6.20E-10 1.42E-06
vg0619892255 sf0619891258 6 19892255 4.20E-09 8.20E-09
vg0717272423 sf0717271430 7 17272423 4.37E-09 1.79E-06
vg0706567685 sf0706566690 7 6567685 1.64E-08 7.48E-08
vg0606584760 sf0606583761 6 6584760 1.00E-07 NA
vg0130989284 sf0130988240 1 30989284 1.44E-07 1.94E-06
vg0906765331 sf0906764331 9 6765331 3.09E-06 3.28E-06
vg0623156624 sf0623155627 6 23156624 3.57E-06 9.64E-07
vg0103191059 sf0103190059 1 3191059 NA 1.65E-06
vg0721519373 sf0721518380 7 21519373 NA 1.83E-06
vg0220342684 sf0220336816 2 20342684 NA 1.90E-06
vg1117421514 sf1116955368 11 17421514 NA 3.01E-06
vg1120941458 sf1120475361 11 20941458 NA 4.45E-06
vg0518660776 sf0518598259 5 18660776 NA 4.61E-06
vg1217503845 sf1217497800 12 17503845 NA 4.85E-06