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 mr1096 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 1.42E-122 1.14E-42
vg0610645257 sf0610644258 6 10645257 2.61E-89 1.08E-29
vg0310439798 sf0310438714 3 10439798 1.04E-58 NA
vg0717186329 sf0717185336 7 17186329 3.55E-58 NA
vg0233932146 sf0233926277 2 33932146 5.77E-58 NA
vg0616574004 sf0616573006 6 16574004 6.66E-58 1.31E-08
vg0617615944 sf0617614947 6 17615944 1.98E-50 3.76E-07
vg0610763769 sf0610762770 6 10763769 NA 9.16E-19
vg0610539571 sf0610538572 6 10539571 NA 1.38E-13
vg0610679715 sf0610678716 6 10679715 NA 1.59E-13
vg0609930953 sf0609929954 6 9930953 NA 4.58E-12
vg0610722873 sf0610721874 6 10722873 NA 4.06E-11
vg0611127099 sf0611126100 6 11127099 NA 4.30E-10
vg0610442214 sf0610441215 6 10442214 NA 7.83E-10
vg0616988304 sf0616987307 6 16988304 NA 1.48E-09
vg0611845202 sf0611856608 6 11845202 NA 1.85E-08
vg0611818263 sf0611817264 6 11818263 NA 4.91E-08
vg0610152420 sf0610151421 6 10152420 NA 9.02E-08
vg0618988041 sf0618987044 6 18988041 NA 3.63E-07
vg0615048733 sf0615047734 6 15048733 NA 4.75E-07
vg0613339384 sf0613338385 6 13339384 NA 5.11E-07
vg0616593098 sf0616592100 6 16593098 NA 9.15E-07
vg0122725848 sf0122724804 1 22725848 NA 9.62E-07
vg0613288089 sf0613287090 6 13288089 NA 1.66E-06
vg0612262780 sf0612261781 6 12262780 NA 2.15E-06
vg0614785443 sf0614784444 6 14785443 NA 2.21E-06
vg0610776489 sf0610775490 6 10776489 NA 2.39E-06
vg0617608061 sf0617607064 6 17608061 NA 2.51E-06