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 mr1121 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
vg0610567030 sf0610566031 6 10567030 1.24E-38 6.61E-27
vg0610874933 sf0610873934 6 10874933 3.13E-14 3.68E-10
vg0610278152 sf0610277153 6 10278152 8.51E-14 3.54E-14
vg0611970043 sf0611969044 6 11970043 1.03E-12 6.64E-09
vg0610587020 sf0610586021 6 10587020 1.16E-12 2.52E-09
vg0611098730 sf0611097731 6 11098730 1.52E-12 1.28E-11
vg0610684751 sf0610683752 6 10684751 4.06E-11 1.62E-07
vg0615048731 sf0615047732 6 15048731 2.07E-10 1.58E-08
vg0610752378 sf0610751379 6 10752378 5.82E-10 1.87E-09
vg0610455817 sf0610454818 6 10455817 6.76E-10 1.42E-07
vg0610116533 sf0610115534 6 10116533 8.40E-10 1.56E-07
vg0619254847 sf0619253850 6 19254847 2.11E-09 5.14E-07
vg0610463202 sf0610462203 6 10463202 2.66E-09 6.69E-07
vg0139756203 sf0139755160 1 39756203 3.86E-09 1.74E-06
vg0611340585 sf0611339586 6 11340585 5.49E-09 4.78E-08
vg0613062563 sf0613061564 6 13062563 1.31E-08 9.79E-08
vg0610642043 sf0610641044 6 10642043 1.67E-08 2.62E-09
vg0717601057 sf0717600064 7 17601057 8.33E-08 1.53E-06
vg0610611566 sf0610610567 6 10611566 8.53E-08 1.68E-07
vg0617636577 sf0617635580 6 17636577 3.27E-07 1.46E-06
vg0611210886 sf0611209887 6 11210886 9.53E-07 3.69E-06
vg0612288311 sf0612287312 6 12288311 3.53E-06 2.62E-07
vg0410126589 sf0410117286 4 10126589 NA 2.27E-07
vg0613063833 sf0613062834 6 13063833 NA 4.23E-07