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 mr1933 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
vg0331273085 sf0331265970 3 31273085 2.54E-39 8.98E-13
vg0222747179 sf0222741310 2 22747179 2.47E-26 5.95E-08
vg0524619804 sf0524557224 5 24619804 1.13E-25 NA
vg1213524250 sf1213521588 12 13524250 1.39E-25 1.84E-07
vg0208886817 sf0208886815 2 8886817 3.66E-25 NA
vg0107647091 sf0107646091 1 7647091 4.30E-23 1.42E-07
vg0222833455 sf0222827586 2 22833455 NA 5.31E-09
vg0222746228 sf0222740359 2 22746228 NA 3.44E-08
vg0331256576 sf0331249461 3 31256576 NA 4.74E-08
vg0423407379 sf0423222234 4 23407379 NA 4.01E-07
vg0319749387 sf0319747898 3 19749387 NA 6.92E-07
vg0725325993 sf0725324999 7 25325993 NA 1.40E-06
vg0621417288 sf0621416291 6 21417288 NA 1.57E-06
vg0723120973 sf0723119980 7 23120973 NA 1.87E-06
vg0401805399 sf0401800994 4 1805399 NA 2.32E-06
vg0910355345 sf0910354344 9 10355345 NA 3.23E-06
vg0527638870 sf0527576227 5 27638870 NA 3.29E-06
vg0528494070 sf0528431425 5 28494070 NA 3.40E-06
vg0724515913 sf0724514919 7 24515913 NA 4.06E-06
vg0411929663 sf0411920374 4 11929663 NA 4.67E-06
vg0133070921 sf0133069877 1 33070921 NA 4.75E-06
vg0910354469 sf0910353468 9 10354469 NA 5.52E-06