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 mr1240 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
vg0222679274 sf0222673405 2 22679274 1.47E-44 3.40E-22
vg0907026290 sf0907025290 9 7026290 7.87E-27 2.59E-12
vg1110425815 sf1110420360 11 10425815 2.75E-26 1.10E-08
vg0526722696 sf0526660054 5 26722696 3.94E-26 8.01E-06
vg0110304750 sf0110303726 1 10304750 7.93E-26 4.64E-06
vg0222735698 sf0222729829 2 22735698 4.04E-25 6.54E-08
vg0435114498 sf0434929380 4 35114498 8.70E-25 7.48E-08
vg0222738600 sf0222732731 2 22738600 3.45E-24 2.05E-07
vg0817799843 sf0817797130 8 17799843 8.51E-24 9.34E-08
vg0306029913 sf0306028913 3 6029913 2.45E-23 9.65E-08
vg0616706040 sf0616705042 6 16706040 8.18E-22 3.77E-09
vg0316147114 sf0316145761 3 16147114 2.60E-21 1.76E-07
vg0235325400 sf0235319531 2 35325400 2.35E-20 1.09E-07
vg1118531424 sf1118065283 11 18531424 8.63E-19 9.34E-08
vg0222722554 sf0222716685 2 22722554 NA 1.86E-09
vg0222271516 sf0222265647 2 22271516 NA 5.60E-09
vg0222952563 sf0222946694 2 22952563 NA 2.58E-08
vg1016331604 sf1016260380 10 16331604 NA 3.94E-08
vg0905862681 sf0905861681 9 5862681 NA 4.37E-08
vg0709837237 sf0709836243 7 9837237 NA 6.07E-08
vg0626215270 sf0626214273 6 26215270 NA 7.04E-08
vg0121803138 sf0121802093 1 21803138 NA 9.65E-08
vg1218360623 sf1218332059 12 18360623 NA 1.60E-07
vg1223504725 sf1223471185 12 23504725 NA 2.02E-07
vg0421291212 sf0421119266 4 21291212 NA 9.60E-07
vg0304642911 sf0304641913 3 4642911 NA 8.54E-06