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 mr1422 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
vg0610271266 sf0610270267 6 10271266 4.44E-32 2.40E-11
vg0719601158 sf0719600165 7 19601158 3.82E-29 2.14E-07
vg0315145562 sf0315144209 3 15145562 1.02E-27 NA
vg0519832584 sf0519770060 5 19832584 4.52E-27 NA
vg0107081953 sf0107080953 1 7081953 1.48E-26 NA
vg0310758468 sf0310757384 3 10758468 2.56E-22 1.13E-06
vg0132480676 sf0132479632 1 32480676 2.04E-20 NA
vg0107079944 sf0107078944 1 7079944 4.14E-19 6.04E-07
vg0109353965 sf0109352941 1 9353965 NA 1.63E-09
vg0610760333 sf0610759334 6 10760333 NA 1.54E-08
vg0629530652 sf0629529654 6 29530652 NA 3.63E-07
vg1217212698 sf1217206653 12 17212698 NA 4.81E-07
vg0613868213 sf0613867214 6 13868213 NA 9.35E-07
vg0610183383 sf0610182384 6 10183383 NA 9.57E-07
vg0719969117 sf0719968124 7 19969117 NA 1.14E-06
vg0610635525 sf0610634526 6 10635525 NA 1.63E-06
vg1217896441 sf1217867875 12 17896441 NA 4.29E-06