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
vg0432188448 sf0432003340 4 32188448 1.15E-09 3.61E-09
vg0222531687 sf0222525818 2 22531687 1.13E-08 1.12E-09
vg0222833455 sf0222827586 2 22833455 1.90E-08 7.38E-07
vg0910545581 sf0910544580 9 10545581 4.79E-08 8.44E-07
vg0220960199 sf0220954331 2 20960199 4.83E-08 7.00E-08
vg0108533994 sf0108532994 1 8533994 5.55E-08 2.06E-06
vg1224514466 sf1224480920 12 24514466 9.82E-08 3.22E-06
vg0709675216 sf0709674222 7 9675216 1.08E-07 3.83E-06
vg0221025908 sf0221020040 2 21025908 1.40E-07 7.63E-09
vg0121574351 sf0121573306 1 21574351 1.93E-07 6.75E-08
vg0224228628 sf0224222759 2 24228628 8.73E-07 5.20E-07
vg0107057661 sf0107056661 1 7057661 9.59E-07 4.13E-06
vg1115847531 sf1115383841 11 15847531 1.63E-06 4.89E-06
vg0124141412 sf0124140368 1 24141412 1.72E-06 3.97E-06
vg0519295480 sf0519232964 5 19295480 3.15E-06 4.87E-06
vg0223741023 sf0223735154 2 23741023 4.49E-06 3.27E-06
vg1126820959 sf1126349346 11 26820959 4.81E-06 4.75E-06
vg0825594684 sf0825591970 8 25594684 7.94E-06 1.40E-06
vg1002828516 sf1002827493 10 2828516 9.82E-06 3.15E-06
vg0221010130 sf0221004262 2 21010130 NA 2.59E-06
vg0901739971 sf0901738971 9 1739971 NA 4.25E-06