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 mr1090 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
vg0610642844 sf0610641845 6 10642844 1.21E-123 7.16E-51
vg0610608095 sf0610607096 6 10608095 1.13E-122 7.51E-53
vg0616519927 sf0616518929 6 16519927 6.37E-64 NA
vg0709180653 sf0709179659 7 9180653 3.91E-60 NA
vg0717252215 sf0717251222 7 17252215 4.10E-60 NA
vg0423817329 sf0423632186 4 23817329 3.79E-59 NA
vg0610539571 sf0610538572 6 10539571 NA 4.46E-43
vg0610722873 sf0610721874 6 10722873 NA 1.27E-21
vg0610763769 sf0610762770 6 10763769 NA 1.21E-15
vg0610679715 sf0610678716 6 10679715 NA 3.10E-13
vg0610723836 sf0610722837 6 10723836 NA 1.11E-12
vg0610118930 sf0610117931 6 10118930 NA 3.56E-11
vg0609926308 sf0609925309 6 9926308 NA 1.52E-10
vg0615774699 sf0615773701 6 15774699 NA 5.61E-10
vg0609976964 sf0609975965 6 9976964 NA 1.24E-09
vg0610645391 sf0610644392 6 10645391 NA 6.24E-09
vg0611081410 sf0611080411 6 11081410 NA 1.51E-08
vg0403922278 sf0403917884 4 3922278 NA 1.70E-08
vg0611127784 sf0611126785 6 11127784 NA 1.95E-08
vg0610146246 sf0610145247 6 10146246 NA 2.61E-08
vg0610443927 sf0610442928 6 10443927 NA 3.74E-08
vg0610082555 sf0610081556 6 10082555 NA 4.33E-08
vg0610531607 sf0610530608 6 10531607 NA 1.09E-07
vg0609609548 sf0609608549 6 9609548 NA 2.01E-07
vg0124099244 sf0124098200 1 24099244 NA 2.07E-07
vg0610495466 sf0610494467 6 10495466 NA 2.47E-07
vg0615048733 sf0615047734 6 15048733 NA 2.48E-07
vg0209835682 sf0209835680 2 9835682 NA 3.05E-07
vg0609930953 sf0609929954 6 9930953 NA 3.35E-07