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 mr1344 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
vg0715701891 sf0715700898 7 15701891 7.19E-09 6.85E-07
vg1016075640 sf1016004412 10 16075640 1.05E-07 7.47E-08
vg0912951105 sf0912950104 9 12951105 1.12E-07 2.81E-07
vg1014161943 sf1014090709 10 14161943 1.52E-07 1.43E-08
vg0715976780 sf0715975787 7 15976780 2.10E-07 3.93E-06
vg0415587826 sf0415578513 4 15587826 2.68E-07 7.27E-08
vg0403394800 sf0403390403 4 3394800 3.48E-07 1.73E-07
vg1017311816 sf1017240589 10 17311816 5.74E-07 7.69E-06
vg0910981641 sf0910980640 9 10981641 5.90E-07 1.78E-06
vg0918621961 sf0918620960 9 18621961 8.65E-07 4.28E-06
vg0817359828 sf0817357114 8 17359828 1.02E-06 1.78E-06
vg0714102413 sf0714101420 7 14102413 1.03E-06 1.66E-06
vg1016452188 sf1016380962 10 16452188 1.04E-06 4.06E-06
vg0715326938 sf0715325945 7 15326938 1.10E-06 NA
vg1204232518 sf1204231506 12 4232518 1.63E-06 2.21E-06
vg0415780925 sf0415608959 4 15780925 2.75E-06 1.80E-07
vg1216729892 sf1216723846 12 16729892 8.94E-06 2.30E-06