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 mr1365 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
vg0710448830 sf0710447836 7 10448830 3.16E-07 3.16E-07
vg0820969276 sf0820966563 8 20969276 3.50E-07 3.50E-07
vg0103392356 sf0103391356 1 3392356 1.13E-06 1.13E-06
vg0103381628 sf0103380628 1 3381628 1.45E-06 1.45E-06
vg0431411704 sf0431226602 4 31411704 1.52E-06 1.52E-06
vg1210206055 sf1210203466 12 10206055 1.80E-06 1.80E-06
vg1109631523 sf1109626100 11 9631523 2.24E-06 2.24E-06
vg1007900043 sf1007915653 10 7900043 3.06E-06 3.06E-06
vg0710393280 sf0710392286 7 10393280 3.69E-06 3.69E-06
vg0431472905 sf0431287803 4 31472905 4.13E-06 4.13E-06
vg0200505558 sf0200505558 2 505558 4.56E-06 4.56E-06
vg0719981901 sf0719980908 7 19981901 4.80E-06 4.80E-06