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 mr1908 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
vg1121559924 sf1121093801 11 21559924 5.17E-10 5.17E-10
vg0304064339 sf0304063335 3 4064339 9.09E-08 9.10E-08
vg1121346183 sf1120880060 11 21346183 1.51E-07 1.51E-07
vg0325666499 sf0325664517 3 25666499 2.54E-07 2.54E-07
vg0226040606 sf0226034737 2 26040606 4.97E-07 4.97E-07
vg0904231862 sf0904230862 9 4231862 5.97E-07 5.97E-07
vg0901631141 sf0901630141 9 1631141 8.31E-07 8.30E-07
vg0608569347 sf0608568348 6 8569347 9.90E-07 9.90E-07
vg0219894442 sf0219888574 2 19894442 1.36E-06 1.36E-06
vg0202609273 sf0202573670 2 2609273 1.88E-06 1.88E-06
vg1200182957 sf1200181957 12 182957 1.91E-06 1.91E-06
vg1121374252 sf1120908129 11 21374252 2.05E-06 2.05E-06
vg0720602295 sf0720601302 7 20602295 2.31E-06 2.31E-06
vg0901405183 sf0901404183 9 1405183 2.75E-06 2.75E-06
vg0112495464 sf0112494438 1 12495464 3.08E-06 3.08E-06
vg1122296817 sf1121830688 11 22296817 4.03E-06 4.03E-06
vg0629694174 sf0629693176 6 29694174 4.06E-06 4.06E-06
vg1203639038 sf1203638037 12 3639038 4.27E-06 4.27E-06
vg1109252886 sf1109247463 11 9252886 4.47E-06 4.47E-06
vg1122081867 sf1121615738 11 22081867 4.76E-06 4.76E-06