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 mr1991 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
vg1220124236 sf1220095678 12 20124236 7.07E-78 4.74E-22
vg1220405263 sf1220376705 12 20405263 4.19E-76 3.71E-23
vg0128519132 sf0128518087 1 28519132 9.18E-63 2.30E-07
vg0128519107 sf0128518062 1 28519107 1.10E-62 1.77E-07
vg0224733131 sf0224727262 2 24733131 2.67E-60 NA
vg0307269312 sf0307268310 3 7269312 6.67E-60 1.66E-06
vg0722677897 sf0722676904 7 22677897 2.36E-59 NA
vg0807262913 sf0807261918 8 7262913 1.44E-55 2.18E-06
vg0311298528 sf0311297246 3 11298528 1.91E-55 3.40E-06
vg1224722880 sf1224689334 12 24722880 4.12E-54 2.85E-06
vg1220380598 sf1220352040 12 20380598 NA 2.85E-09
vg1220185655 sf1220157097 12 20185655 NA 4.92E-08
vg0128531967 sf0128530922 1 28531967 NA 4.57E-07
vg1127840328 sf1127368714 11 27840328 NA 9.84E-07
vg0222144498 sf0222138629 2 22144498 NA 1.47E-06
vg1220404712 sf1220376154 12 20404712 NA 3.12E-06
vg1217437473 sf1217431428 12 17437473 NA 3.34E-06
vg1217341046 sf1217335001 12 17341046 NA 4.88E-06