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 mr1783 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
vg0709984451 sf0709983457 7 9984451 3.40E-07 3.40E-07
vg1007900043 sf1007915653 10 7900043 3.52E-07 3.52E-07
vg1109631523 sf1109626100 11 9631523 3.74E-07 3.74E-07
vg0431411704 sf0431226602 4 31411704 8.08E-07 8.08E-07
vg0324647482 sf0324645561 3 24647482 8.34E-07 8.33E-07
vg1210189485 sf1210186896 12 10189485 8.74E-07 8.74E-07
vg0710985476 sf0710984482 7 10985476 1.38E-06 1.38E-06
vg0431472905 sf0431287803 4 31472905 1.44E-06 1.44E-06
vg1107375253 sf1107370998 11 7375253 2.08E-06 2.08E-06
vg0820865298 sf0820862585 8 20865298 2.29E-06 2.30E-06
vg1215178307 sf1215175643 12 15178307 2.43E-06 2.43E-06
vg0413906303 sf0413897020 4 13906303 4.24E-06 4.24E-06
vg0229918162 sf0229912293 2 29918162 9.58E-06 9.58E-06