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 mr1525 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
vg0405540593 sf0405536034 4 5540593 4.12E-14 4.13E-14
vg0405735471 sf0405730910 4 5735471 2.94E-13 2.94E-13
vg0405481249 sf0405476690 4 5481249 6.70E-13 6.66E-13
vg0405531121 sf0405526562 4 5531121 3.48E-11 3.36E-11
vg0410128864 sf0410119561 4 10128864 3.54E-08 3.55E-08
vg0816175621 sf0816172907 8 16175621 1.42E-07 1.42E-07
vg0405832497 sf0405827936 4 5832497 2.87E-07 2.87E-07
vg1200579778 sf1200578778 12 579778 1.22E-06 1.22E-06
vg0219956044 sf0219950176 2 19956044 1.76E-06 1.76E-06
vg1117531985 sf1117065840 11 17531985 2.10E-06 2.10E-06
vg0405151676 sf0405147118 4 5151676 2.16E-06 2.16E-06
vg0405298921 sf0405294362 4 5298921 2.19E-06 2.17E-06
vg1206236301 sf1206235191 12 6236301 4.91E-06 4.92E-06
vg0134310167 sf0134309124 1 34310167 7.51E-06 7.51E-06