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 mr1424 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
vg1214217183 sf1214214523 12 14217183 1.55E-06 1.55E-06
vg0203000556 sf0203000554 2 3000556 2.17E-06 2.17E-06
vg0408147564 sf0408142838 4 8147564 2.25E-06 2.25E-06
vg0228504159 sf0228498290 2 28504159 2.97E-06 2.96E-06
vg1127382510 sf1126910897 11 27382510 3.50E-06 3.50E-06
vg1127289636 sf1126818023 11 27289636 4.50E-06 4.51E-06
vg1117135476 sf1116669328 11 17135476 4.99E-06 4.98E-06
vg0431515534 sf0431330433 4 31515534 8.44E-06 8.43E-06