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 mr1039 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
vg0506849318 sf0506849260 5 6849318 3.27E-137 2.46E-90
vg0506870338 sf0506870280 5 6870338 4.65E-133 1.00E-90
vg1001247140 sf1001246117 10 1247140 3.37E-48 7.16E-16
vg0506946098 sf0506946040 5 6946098 5.03E-46 8.14E-14
vg0512332611 sf0512332541 5 12332611 7.61E-46 5.03E-20
vg0506870368 sf0506870310 5 6870368 1.11E-45 5.82E-17
vg0509447947 sf0509447876 5 9447947 1.33E-43 1.91E-16
vg0506835795 sf0506835737 5 6835795 1.73E-43 3.07E-10
vg0506874665 sf0506874607 5 6874665 2.74E-43 5.09E-18
vg0506881909 sf0506881851 5 6881909 4.60E-43 1.36E-13
vg0506835494 sf0506835436 5 6835494 1.10E-42 1.69E-11
vg0506835785 sf0506835727 5 6835785 4.38E-40 3.49E-06
vg0514650910 sf0514593453 5 14650910 7.90E-40 2.59E-13
vg1009362967 sf1009291788 10 9362967 1.07E-38 6.02E-15
vg0507885416 sf0507885357 5 7885416 2.76E-33 1.23E-09
vg0506708732 sf0506708674 5 6708732 2.99E-31 5.26E-14
vg0507782081 sf0507782022 5 7782081 3.35E-31 2.62E-07
vg0506100456 sf0506100395 5 6100456 2.25E-28 2.14E-09
vg0509088193 sf0509088121 5 9088193 1.49E-27 8.13E-10
vg0506884765 sf0506884707 5 6884765 NA 1.11E-19
vg0507003092 sf0507003034 5 7003092 NA 9.92E-13
vg0506632469 sf0506632410 5 6632469 NA 5.32E-11
vg0233906724 sf0233900855 2 33906724 NA 5.38E-10
vg0505412165 sf0505412143 5 5412165 NA 1.77E-09
vg0506893511 sf0506893453 5 6893511 NA 4.67E-08
vg0507039642 sf0507039584 5 7039642 NA 8.25E-08
vg0326930904 sf0326923957 3 26930904 NA 1.79E-07
vg0508129211 sf0508129151 5 8129211 NA 1.85E-07
vg0516207085 sf0516149567 5 16207085 NA 2.54E-07
vg1021109650 sf1021038129 10 21109650 NA 3.37E-07