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 mr1671 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
vg0304338025 sf0304337027 3 4338025 1.66E-11 NA
vg0815939205 sf0815936491 8 15939205 1.93E-11 NA
vg0102110704 sf0102109704 1 2110704 4.48E-11 NA
vg0810553279 sf0810552283 8 10553279 1.08E-10 NA
vg0139831768 sf0139830725 1 39831768 1.41E-10 NA
vg0726378569 sf0726377575 7 26378569 9.95E-10 1.99E-06
vg0810228654 sf0810227658 8 10228654 4.16E-07 2.89E-06