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 mr1698 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
vg0234351254 sf0234345385 2 34351254 1.77E-28 1.17E-06
vg1121988122 sf1121521993 11 21988122 4.51E-27 7.73E-08
vg0717369423 sf0717368430 7 17369423 5.15E-27 4.39E-07
vg0717364385 sf0717363392 7 17364385 7.31E-27 3.72E-07
vg0717415215 sf0717414222 7 17415215 1.93E-26 2.76E-06
vg1015191238 sf1015120006 10 15191238 2.85E-26 1.44E-06
vg0307075857 sf0307074855 3 7075857 8.41E-26 5.24E-06
vg0904244136 sf0904243136 9 4244136 3.38E-25 3.17E-06
vg0121627643 sf0121626598 1 21627643 3.57E-25 5.14E-07
vg0128531441 sf0128530396 1 28531441 4.68E-25 4.91E-06
vg0404270383 sf0404265990 4 4270383 NA 1.33E-09
vg0404048007 sf0404043614 4 4048007 NA 5.84E-07
vg0400996445 sf0400991997 4 996445 NA 6.35E-07
vg0404504944 sf0404500548 4 4504944 NA 1.20E-06
vg0426445210 sf0426260083 4 26445210 NA 3.33E-06
vg1212822297 sf1212819636 12 12822297 NA 3.56E-06
vg1117422908 sf1116956762 11 17422908 NA 7.82E-06