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 2.50E-125 1.04E-72
vg0506871793 sf0506871735 5 6871793 1.58E-118 2.72E-70
vg1001247140 sf1001246117 10 1247140 2.50E-52 3.09E-15
vg1009362967 sf1009291788 10 9362967 3.43E-45 9.03E-15
vg0506840667 sf0506840609 5 6840667 6.05E-44 2.74E-13
vg0513833782 sf0513776326 5 13833782 5.29E-42 3.03E-15
vg0512332611 sf0512332541 5 12332611 1.04E-41 2.53E-16
vg0506944661 sf0506944603 5 6944661 2.29E-41 7.04E-13
vg0509650627 sf0509650556 5 9650627 7.46E-39 8.07E-14
vg0506866456 sf0506866398 5 6866456 9.21E-38 1.78E-14
vg0514684611 sf0514627154 5 14684611 7.59E-37 3.64E-09
vg0507837679 sf0507837620 5 7837679 3.58E-33 3.60E-10
vg0508975741 sf0508975669 5 8975741 6.22E-29 7.15E-09
vg0506708732 sf0506708674 5 6708732 2.83E-28 8.26E-10
vg0506884765 sf0506884707 5 6884765 NA 3.13E-16
vg0507003092 sf0507003034 5 7003092 NA 4.84E-12
vg0506060649 sf0506060588 5 6060649 NA 3.58E-10
vg0506631795 sf0506631736 5 6631795 NA 2.16E-08
vg0505429323 sf0505429301 5 5429323 NA 5.10E-08
vg0127822608 sf0127821564 1 27822608 NA 6.93E-08
vg0507977136 sf0507977077 5 7977136 NA 3.87E-07
vg0506924589 sf0506924531 5 6924589 NA 4.23E-07
vg0331312141 sf0331305026 3 31312141 NA 4.59E-07
vg0526219303 sf0526156667 5 26219303 NA 7.05E-07
vg0325324679 sf0325322760 3 25324679 NA 8.08E-07
vg0500189212 sf0500189212 5 189212 NA 1.17E-06
vg0915440900 sf0915439899 9 15440900 NA 1.40E-06