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 mr1119 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
vg0222679274 sf0222673405 2 22679274 7.01E-47 2.61E-20
vg0222675535 sf0222669666 2 22675535 2.93E-45 5.00E-22
vg0507023861 sf0507023803 5 7023861 5.86E-27 2.23E-07
vg0526722696 sf0526660054 5 26722696 7.64E-27 7.16E-07
vg0518201525 sf0518141011 5 18201525 1.51E-26 1.09E-07
vg1110425815 sf1110420360 11 10425815 4.25E-26 5.60E-09
vg0505887711 sf0505887649 5 5887711 6.46E-26 2.56E-08
vg0306047262 sf0306046262 3 6047262 1.27E-23 2.12E-08
vg0818212763 sf0818210050 8 18212763 3.93E-23 2.66E-08
vg0500664660 sf0500664660 5 664660 7.03E-23 7.21E-08
vg0825750246 sf0825747532 8 25750246 3.81E-22 3.05E-07
vg0907026290 sf0907025290 9 7026290 6.03E-22 1.68E-08
vg1117963441 sf1117497299 11 17963441 1.44E-19 2.95E-07
vg0222271516 sf0222265647 2 22271516 1.88E-17 1.68E-08
vg0222952563 sf0222946694 2 22952563 NA 3.93E-10
vg0222722554 sf0222716685 2 22722554 NA 3.00E-09
vg0709837237 sf0709836243 7 9837237 NA 1.48E-08
vg0315713125 sf0315711772 3 15713125 NA 3.64E-08
vg0822600721 sf0822598008 8 22600721 NA 4.95E-08
vg0922265212 sf0922264731 9 22265212 NA 4.99E-08
vg0140888130 sf0140887087 1 40888130 NA 7.70E-08
vg1204507349 sf1204506337 12 4507349 NA 8.10E-08
vg1209218924 sf1209216333 12 9218924 NA 9.96E-08
vg1021149005 sf1021077484 10 21149005 NA 1.46E-07
vg1016331604 sf1016260380 10 16331604 NA 1.60E-07
vg0609907276 sf0609906277 6 9907276 NA 2.05E-07
vg0139710848 sf0139709805 1 39710848 NA 2.11E-07
vg0223419298 sf0223413429 2 23419298 NA 4.34E-06
vg0315922266 sf0315920913 3 15922266 NA 4.91E-06
vg1006265706 sf1006281329 10 6265706 NA 8.47E-06