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 mr1375 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
vg0137855094 sf0137854051 1 37855094 4.76E-10 4.76E-10
vg1121706044 sf1121239921 11 21706044 1.67E-07 1.67E-07
vg0714342439 sf0714341446 7 14342439 2.57E-06 2.57E-06
vg1219118839 sf1219090275 12 19118839 3.48E-06 3.48E-06
vg0225208298 sf0225202429 2 25208298 3.79E-06 3.79E-06
vg1105544663 sf1105540415 11 5544663 3.83E-06 3.83E-06