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 mr1815 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
vg0122730523 sf0122729479 1 22730523 4.47E-09 1.02E-06
vg1220427559 sf1220399001 12 20427559 8.30E-08 1.07E-06
vg0501127004 sf0501126988 5 1127004 8.45E-08 NA
vg0501133128 sf0501133112 5 1133128 4.54E-07 8.52E-06
vg0332412085 sf0332404957 3 32412085 1.81E-06 3.23E-06
vg1218022863 sf1217994299 12 18022863 2.62E-06 4.12E-06
vg0117362788 sf0117361742 1 17362788 4.00E-06 2.26E-06
vg0804616740 sf0804615743 8 4616740 4.04E-06 NA
vg0518363321 sf0518302807 5 18363321 9.04E-06 1.11E-06
vg0814004979 sf0814002265 8 14004979 NA 3.46E-06
vg1207220741 sf1207218137 12 7220741 NA 4.94E-06