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
vg0610566343 sf0610565344 6 10566343 1.14E-131 2.66E-43
vg0610481003 sf0610480004 6 10481003 4.52E-103 1.23E-31
vg0616950705 sf0616949708 6 16950705 1.75E-75 NA
vg0719200994 sf0719200001 7 19200994 8.34E-73 NA
vg0612571543 sf0612570544 6 12571543 3.57E-72 NA
vg0707780684 sf0707779689 7 7780684 1.90E-71 NA
vg0304920678 sf0304919680 3 4920678 3.47E-71 NA
vg0613071383 sf0613070384 6 13071383 8.26E-64 2.42E-07
vg0610763769 sf0610762770 6 10763769 NA 9.46E-18
vg0610444069 sf0610443070 6 10444069 NA 7.09E-15
vg0610813890 sf0610812891 6 10813890 NA 2.43E-13
vg0610679715 sf0610678716 6 10679715 NA 1.33E-12
vg0611682950 sf0611681951 6 11682950 NA 1.54E-11
vg0609929059 sf0609928060 6 9929059 NA 2.34E-11
vg0610281727 sf0610280728 6 10281727 NA 3.79E-11
vg0610791449 sf0610790450 6 10791449 NA 1.01E-10
vg0610702326 sf0610701327 6 10702326 NA 3.19E-10
vg0609920142 sf0609919143 6 9920142 NA 2.64E-08
vg0610026311 sf0610025312 6 10026311 NA 2.68E-08
vg0610021419 sf0610020420 6 10021419 NA 4.61E-08
vg0611926589 sf0611925590 6 11926589 NA 4.88E-08
vg0610540785 sf0610539786 6 10540785 NA 8.12E-08
vg0611125709 sf0611124710 6 11125709 NA 1.32E-07
vg0613809145 sf0613808146 6 13809145 NA 1.60E-07
vg0609902440 sf0609901441 6 9902440 NA 2.01E-07
vg0617319066 sf0617318069 6 17319066 NA 3.24E-07
vg0610393322 sf0610392323 6 10393322 NA 7.00E-07
vg0609684472 sf0609683473 6 9684472 NA 8.72E-07
vg0609211711 sf0609210712 6 9211711 NA 1.04E-06
vg0518201525 sf0518141011 5 18201525 NA 2.96E-06