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 mr1068 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
vg0610608095 sf0610607096 6 10608095 2.49E-138 8.35E-53
vg0708747195 sf0708746200 7 8747195 2.88E-63 NA
vg0715669964 sf0715668971 7 15669964 1.35E-62 NA
vg0233932146 sf0233926277 2 33932146 4.53E-62 NA
vg0304920678 sf0304919680 3 4920678 4.53E-61 NA
vg0617821393 sf0617820396 6 17821393 1.64E-52 2.75E-08
vg0610539571 sf0610538572 6 10539571 NA 5.17E-29
vg0610763769 sf0610762770 6 10763769 NA 4.37E-16
vg0610442278 sf0610441279 6 10442278 NA 2.36E-14
vg0610446203 sf0610445204 6 10446203 NA 1.60E-12
vg0609930953 sf0609929954 6 9930953 NA 4.79E-11
vg0610722873 sf0610721874 6 10722873 NA 5.22E-11
vg0610412517 sf0610411518 6 10412517 NA 7.47E-11
vg0609926308 sf0609925309 6 9926308 NA 6.69E-10
vg0610114523 sf0610113524 6 10114523 NA 1.53E-09
vg0610468695 sf0610467696 6 10468695 NA 3.93E-09
vg0611127784 sf0611126785 6 11127784 NA 6.39E-09
vg0615774699 sf0615773701 6 15774699 NA 9.41E-09
vg0610393322 sf0610392323 6 10393322 NA 3.10E-08
vg0617826668 sf0617825671 6 17826668 NA 3.38E-08
vg0610281727 sf0610280728 6 10281727 NA 4.77E-08
vg0403922278 sf0403917884 4 3922278 NA 6.42E-08
vg0609978811 sf0609977812 6 9978811 NA 7.11E-08
vg0615048733 sf0615047734 6 15048733 NA 7.26E-08
vg0613057898 sf0613056899 6 13057898 NA 1.22E-07
vg0610645391 sf0610644392 6 10645391 NA 1.55E-07