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 mr1720 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
vg1204807699 sf1204806684 12 4807699 2.24E-11 4.19E-08
vg1204091810 sf1204090798 12 4091810 3.37E-11 3.68E-08
vg0720805926 sf0720804933 7 20805926 2.78E-10 1.13E-08
vg1222490179 sf1222456618 12 22490179 1.04E-09 4.76E-06
vg0700834658 sf0700833658 7 834658 1.17E-09 3.70E-06
vg1204796430 sf1204795415 12 4796430 1.35E-09 8.75E-07
vg0331901458 sf0331894335 3 31901458 4.64E-09 NA
vg1204323457 sf1204322445 12 4323457 8.10E-07 6.27E-07
vg0729064560 sf0729063568 7 29064560 NA 4.66E-06