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 mr1111 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
vg0610567118 sf0610566119 6 10567118 8.31E-117 2.01E-42
vg0610608095 sf0610607096 6 10608095 1.35E-114 8.30E-44
vg0304920678 sf0304919680 3 4920678 5.50E-61 NA
vg0233932146 sf0233926277 2 33932146 1.76E-59 NA
vg0615150907 sf0615149908 6 15150907 2.11E-57 NA
vg0428608405 sf0428423256 4 28608405 3.43E-57 NA
vg0610532672 sf0610531673 6 10532672 NA 1.71E-20
vg0610752378 sf0610751379 6 10752378 NA 4.18E-17
vg0610763769 sf0610762770 6 10763769 NA 1.11E-14
vg0610444069 sf0610443070 6 10444069 NA 3.95E-14
vg0610134394 sf0610133395 6 10134394 NA 7.16E-12
vg0610685711 sf0610684712 6 10685711 NA 5.04E-11
vg0610358849 sf0610357850 6 10358849 NA 1.02E-10
vg0611127784 sf0611126785 6 11127784 NA 9.08E-08
vg0619171840 sf0619170843 6 19171840 NA 1.84E-07
vg0610723836 sf0610722837 6 10723836 NA 2.98E-07
vg0609929059 sf0609928060 6 9929059 NA 3.69E-07
vg0610082555 sf0610081556 6 10082555 NA 4.22E-07
vg0610630577 sf0610629578 6 10630577 NA 4.25E-07
vg0611643383 sf0611642384 6 11643383 NA 4.47E-07
vg0615907055 sf0615906057 6 15907055 NA 4.55E-07
vg0617622905 sf0617621908 6 17622905 NA 5.08E-07
vg0610495424 sf0610494425 6 10495424 NA 5.94E-07
vg0613339384 sf0613338385 6 13339384 NA 1.01E-06
vg0614785443 sf0614784444 6 14785443 NA 1.12E-06
vg0612980757 sf0612979758 6 12980757 NA 1.58E-06
vg0402824534 sf0402820139 4 2824534 NA 1.93E-06
vg0617644616 sf0617643619 6 17644616 NA 2.99E-06