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 mr1372 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
vg1111043318 sf1111037635 11 11043318 7.07E-08 2.65E-06
vg0712648528 sf0712647535 7 12648528 1.05E-07 7.56E-07
vg1119100956 sf1118634644 11 19100956 1.43E-07 4.67E-06
vg1002941120 sf1002940097 10 2941120 2.89E-07 9.56E-07
vg0406883539 sf0406878798 4 6883539 2.98E-07 5.11E-07
vg0327981236 sf0327974290 3 27981236 7.22E-07 4.17E-06
vg0722504993 sf0722504000 7 22504993 7.30E-07 3.75E-06
vg0910768444 sf0910767443 9 10768444 1.11E-06 1.91E-06
vg1126786095 sf1126314482 11 26786095 4.07E-06 NA
vg1114873399 sf1114409713 11 14873399 7.45E-06 NA
vg0132161653 sf0132160609 1 32161653 NA 1.49E-06