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 mr1150 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
vg0222725905 sf0222720036 2 22725905 1.08E-64 1.11E-46
vg0222715139 sf0222709270 2 22715139 4.28E-62 1.73E-43
vg0222723400 sf0222717531 2 22723400 1.95E-49 5.20E-35
vg0223077967 sf0223072098 2 23077967 4.88E-16 2.79E-08
vg0224529885 sf0224524016 2 24529885 1.83E-15 4.59E-08
vg0224664402 sf0224658533 2 24664402 3.72E-15 1.63E-12
vg0223077707 sf0223071838 2 23077707 6.13E-14 4.73E-10
vg0221695303 sf0221689434 2 21695303 1.66E-13 1.17E-06
vg0224263868 sf0224257999 2 24263868 1.69E-12 2.83E-06
vg1112606022 sf1112142225 11 12606022 1.39E-11 5.97E-08
vg0222879623 sf0222873754 2 22879623 5.48E-11 4.18E-11
vg0224878279 sf0224872410 2 24878279 1.12E-10 1.23E-07
vg0222729132 sf0222723263 2 22729132 1.31E-10 3.10E-08
vg0222041029 sf0222035160 2 22041029 2.58E-10 6.81E-09
vg0205189046 sf0205189043 2 5189046 4.91E-10 3.99E-07
vg0223166694 sf0223160825 2 23166694 6.28E-10 2.29E-06
vg0225072231 sf0225066362 2 25072231 1.85E-09 2.63E-06
vg0224788519 sf0224782650 2 24788519 3.76E-09 2.24E-07
vg0222987671 sf0222981802 2 22987671 5.93E-09 9.05E-08
vg0224229948 sf0224224079 2 24229948 7.77E-09 1.73E-08
vg0221953494 sf0221947625 2 21953494 1.47E-08 8.73E-08
vg0223720122 sf0223714253 2 23720122 2.01E-08 2.21E-06
vg0224824813 sf0224818944 2 24824813 NA 2.64E-09
vg0222629109 sf0222623240 2 22629109 NA 5.11E-08
vg0222546189 sf0222540320 2 22546189 NA 4.97E-07
vg0407808657 sf0407803925 4 7808657 NA 5.55E-07
vg1111154872 sf1111149189 11 11154872 NA 1.44E-06