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 mr1145 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
vg0719001778 sf0719000785 7 19001778 3.99E-11 1.15E-08
vg0719208938 sf0719207945 7 19208938 4.38E-11 1.78E-10
vg0719140447 sf0719139454 7 19140447 2.58E-10 1.10E-07
vg1201443848 sf1201442848 12 1443848 2.62E-10 4.00E-08
vg1201899563 sf1201898561 12 1899563 7.79E-10 9.67E-07
vg0719140489 sf0719139496 7 19140489 2.24E-09 1.46E-06
vg0719191884 sf0719190891 7 19191884 3.20E-09 5.68E-08
vg1219115474 sf1219086910 12 19115474 7.04E-09 NA
vg0428312965 sf0428127823 4 28312965 7.24E-09 3.83E-06
vg1201963046 sf1201962044 12 1963046 6.97E-08 NA
vg1009414426 sf1009343247 10 9414426 9.28E-07 4.12E-06
vg0517787481 sf0517726967 5 17787481 1.71E-06 3.55E-06
vg0606529256 sf0606528257 6 6529256 NA 1.88E-06
vg0114208344 sf0114207318 1 14208344 NA 2.41E-06
vg0718994741 sf0718993748 7 18994741 NA 4.70E-06