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 mr1445 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
vg0819431872 sf0819429159 8 19431872 8.71E-08 8.71E-08
vg0403579142 sf0403574744 4 3579142 6.35E-07 6.35E-07
vg0416930919 sf0416758961 4 16930919 9.32E-07 9.32E-07
vg0227578016 sf0227572147 2 27578016 9.70E-07 9.70E-07
vg0124089174 sf0124088130 1 24089174 2.43E-06 2.43E-06
vg0431033243 sf0430848127 4 31033243 2.55E-06 2.55E-06
vg0222337580 sf0222331711 2 22337580 2.71E-06 2.71E-06
vg0803730363 sf0803729366 8 3730363 2.98E-06 2.98E-06
vg0220941584 sf0220935716 2 20941584 3.36E-06 3.36E-06
vg0106301158 sf0106300158 1 6301158 3.89E-06 3.89E-06
vg0232543553 sf0232537684 2 32543553 4.33E-06 4.33E-06
vg0219777733 sf0219771865 2 19777733 4.39E-06 4.39E-06
vg0608258762 sf0608257763 6 8258762 4.48E-06 4.48E-06