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 mr1305 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
vg0325710457 sf0325708475 3 25710457 6.18E-38 2.47E-32
vg0325696417 sf0325694435 3 25696417 6.66E-38 1.72E-32
vg0400345487 sf0400344487 4 345487 1.34E-14 2.26E-09
vg1121970827 sf1121504698 11 21970827 4.30E-13 3.28E-07
vg1002067295 sf1002066272 10 2067295 1.22E-12 2.91E-08
vg0222035625 sf0222029756 2 22035625 1.35E-12 4.82E-08
vg1006011150 sf1006027688 10 6011150 2.28E-12 5.36E-08
vg1004789770 sf1004806307 10 4789770 4.93E-12 4.98E-08
vg0229389860 sf0229383991 2 29389860 9.74E-12 9.59E-08
vg0202731072 sf0202731070 2 2731072 3.32E-11 4.05E-09
vg0327423375 sf0327416428 3 27423375 4.64E-11 2.80E-09
vg1012888857 sf1012817672 10 12888857 7.63E-11 3.31E-10
vg0609841754 sf0609840755 6 9841754 9.03E-11 1.65E-08
vg0729677691 sf0729676699 7 29677691 1.13E-10 1.79E-07
vg0220048340 sf0220042472 2 20048340 1.21E-10 2.16E-08
vg1005689732 sf1005706270 10 5689732 2.21E-10 6.02E-08
vg0315495912 sf0315494559 3 15495912 4.95E-10 8.42E-08
vg1212987580 sf1212984919 12 12987580 1.10E-09 6.92E-08
vg0322820996 sf0322819485 3 22820996 2.12E-09 5.87E-08
vg0415028838 sf0415019552 4 15028838 3.34E-09 3.80E-08
vg0225789722 sf0225783853 2 25789722 3.55E-08 1.03E-07
vg0907838282 sf0907837282 9 7838282 NA 1.25E-07