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 mr1632 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
vg0506870338 sf0506870280 5 6870338 1.63E-68 1.56E-48
vg0506946098 sf0506946040 5 6946098 4.08E-60 1.94E-18
vg0506870368 sf0506870310 5 6870368 4.83E-60 3.62E-21
vg0506945693 sf0506945635 5 6945693 4.32E-59 5.04E-18
vg0514684611 sf0514627154 5 14684611 3.18E-50 2.67E-14
vg0514650910 sf0514593453 5 14650910 1.04E-49 6.85E-15
vg0725554561 sf0725553567 7 25554561 3.63E-36 NA
vg0228725979 sf0228720110 2 28725979 4.41E-36 NA
vg0511662961 sf0511662891 5 11662961 6.18E-34 1.07E-18
vg1009362967 sf1009291788 10 9362967 2.92E-32 9.75E-15
vg0507887261 sf0507887202 5 7887261 1.64E-31 1.45E-10
vg0514534416 sf0514476959 5 14534416 NA 1.83E-14
vg0508006957 sf0508006898 5 8006957 NA 7.37E-13
vg1001247140 sf1001246117 10 1247140 NA 9.84E-12
vg0514322241 sf0514264784 5 14322241 NA 2.73E-11
vg0506060649 sf0506060588 5 6060649 NA 6.44E-11
vg0508367063 sf0508366991 5 8367063 NA 2.81E-10
vg0233906724 sf0233900855 2 33906724 NA 7.76E-10
vg0511433628 sf0511433558 5 11433628 NA 5.30E-09
vg0511679660 sf0511679590 5 11679660 NA 2.00E-08
vg0614104823 sf0614103824 6 14104823 NA 2.65E-08
vg0614104820 sf0614103821 6 14104820 NA 2.77E-08
vg0506924589 sf0506924531 5 6924589 NA 7.25E-08
vg0506677994 sf0506677935 5 6677994 NA 8.20E-08
vg0218246948 sf0218241079 2 18246948 NA 9.15E-08
vg0322555893 sf0322554382 3 22555893 NA 1.05E-07
vg0507003092 sf0507003034 5 7003092 NA 1.12E-07
vg1119967965 sf1119501888 11 19967965 NA 3.24E-06
vg0516053930 sf0515996438 5 16053930 NA 9.11E-06