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 mr1065 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 1.80E-137 3.14E-44
vg0610487027 sf0610486028 6 10487027 2.30E-126 2.40E-44
vg0610584498 sf0610583499 6 10584498 2.83E-109 2.38E-35
vg0616950705 sf0616949708 6 16950705 2.78E-83 5.41E-06
vg0719132379 sf0719131386 7 19132379 2.37E-76 NA
vg0304920678 sf0304919680 3 4920678 4.62E-75 NA
vg0627242607 sf0627241610 6 27242607 5.53E-73 NA
vg0617223679 sf0617222682 6 17223679 2.13E-65 1.32E-08
vg0610763769 sf0610762770 6 10763769 NA 9.51E-18
vg0610444069 sf0610443070 6 10444069 NA 8.36E-16
vg0610476284 sf0610475285 6 10476284 NA 3.10E-14
vg0610444115 sf0610443116 6 10444115 NA 6.52E-13
vg0609929059 sf0609928060 6 9929059 NA 1.56E-12
vg0611682950 sf0611681951 6 11682950 NA 4.47E-12
vg0611926589 sf0611925590 6 11926589 NA 3.65E-10
vg0611127099 sf0611126100 6 11127099 NA 3.68E-10
vg0610360687 sf0610359688 6 10360687 NA 9.85E-10
vg0920309265 sf0920308784 9 20309265 NA 4.83E-09
vg0610002230 sf0610001231 6 10002230 NA 1.16E-08
vg0610116533 sf0610115534 6 10116533 NA 2.48E-08
vg0610069455 sf0610068456 6 10069455 NA 8.93E-08
vg0612022465 sf0612021466 6 12022465 NA 1.58E-07
vg0612050111 sf0612049112 6 12050111 NA 1.59E-07
vg0629122299 sf0629121301 6 29122299 NA 2.36E-07
vg0613057898 sf0613056899 6 13057898 NA 2.71E-07
vg0610928548 sf0610927549 6 10928548 NA 3.41E-07
vg0610070186 sf0610069187 6 10070186 NA 4.51E-07
vg0610393322 sf0610392323 6 10393322 NA 6.09E-07
vg0920305662 sf0920305181 9 20305662 NA 8.21E-07
vg0613058999 sf0613058000 6 13058999 NA 4.25E-06