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 mr1110 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 1.56E-81 4.50E-21
vg0610566343 sf0610565344 6 10566343 1.58E-77 3.85E-21
vg0610737234 sf0610736235 6 10737234 6.21E-55 1.36E-16
vg0719200994 sf0719200001 7 19200994 1.46E-46 NA
vg0617620218 sf0617619221 6 17620218 4.51E-46 7.14E-08
vg0613065676 sf0613064677 6 13065676 2.22E-43 2.01E-06
vg0715665434 sf0715664441 7 15665434 1.16E-42 NA
vg0613124807 sf0613123808 6 13124807 1.45E-39 9.38E-07
vg0711377056 sf0711376062 7 11377056 1.61E-36 1.49E-07
vg0617413253 sf0617412256 6 17413253 5.90E-36 NA
vg0610778299 sf0610777300 6 10778299 NA 2.82E-11
vg0611944138 sf0611943139 6 11944138 NA 2.23E-09
vg1008321363 sf1008250225 10 8321363 NA 3.43E-09
vg1006522262 sf1006537885 10 6522262 NA 2.08E-08
vg0610788671 sf0610787672 6 10788671 NA 4.01E-08
vg1009114642 sf1009043503 10 9114642 NA 1.09E-07
vg1009136452 sf1009065313 10 9136452 NA 1.11E-07
vg0407825479 sf0407820747 4 7825479 NA 1.66E-07
vg0610278393 sf0610277394 6 10278393 NA 1.73E-07
vg0615398593 sf0615397594 6 15398593 NA 3.46E-07
vg0610707600 sf0610706601 6 10707600 NA 4.26E-07
vg1007467618 sf1007483241 10 7467618 NA 4.80E-07
vg0613825382 sf0613824383 6 13825382 NA 4.81E-07
vg0610021530 sf0610020531 6 10021530 NA 5.27E-07
vg0610028912 sf0610027913 6 10028912 NA 5.49E-07
vg1007683620 sf1007699229 10 7683620 NA 6.45E-07
vg0615515353 sf0615514355 6 15515353 NA 9.78E-07
vg0614543893 sf0614542894 6 14543893 NA 1.72E-06
vg0700328914 sf0700327914 7 328914 NA 2.36E-06
vg0611127099 sf0611126100 6 11127099 NA 2.48E-06
vg1216843191 sf1216837145 12 16843191 NA 2.65E-06
vg0611682950 sf0611681951 6 11682950 NA 2.72E-06