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 mr1112 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
vg0610559165 sf0610558166 6 10559165 9.18E-95 3.53E-25
vg0610566343 sf0610565344 6 10566343 1.28E-94 7.59E-26
vg0610680325 sf0610679326 6 10680325 1.78E-76 9.48E-21
vg0719200994 sf0719200001 7 19200994 2.10E-59 NA
vg0122402967 sf0122401922 1 22402967 6.04E-55 NA
vg0616950705 sf0616949708 6 16950705 2.06E-54 NA
vg0402287234 sf0402282829 4 2287234 3.05E-52 NA
vg0617383481 sf0617382484 6 17383481 1.08E-45 8.41E-07
vg0610763769 sf0610762770 6 10763769 NA 3.63E-10
vg0609930953 sf0609929954 6 9930953 NA 6.44E-10
vg0610813890 sf0610812891 6 10813890 NA 9.33E-09
vg0611882368 sf0611881369 6 11882368 NA 2.48E-08
vg0610776489 sf0610775490 6 10776489 NA 4.25E-08
vg0610278393 sf0610277394 6 10278393 NA 5.49E-08
vg0617631923 sf0617630926 6 17631923 NA 3.31E-07
vg0609643486 sf0609642487 6 9643486 NA 6.23E-07
vg0610633493 sf0610632494 6 10633493 NA 6.57E-07
vg0614543893 sf0614542894 6 14543893 NA 1.30E-06
vg0610442278 sf0610441279 6 10442278 NA 1.30E-06
vg0609903452 sf0609902453 6 9903452 NA 1.39E-06
vg0617636590 sf0617635593 6 17636590 NA 1.71E-06
vg0613067756 sf0613066757 6 13067756 NA 1.81E-06
vg0611682950 sf0611681951 6 11682950 NA 3.28E-06
vg0610707600 sf0610706601 6 10707600 NA 3.30E-06
vg0116357536 sf0116356510 1 16357536 NA 3.75E-06
vg1017015778 sf1016944550 10 17015778 NA 4.20E-06
vg0711377056 sf0711376062 7 11377056 NA 4.51E-06