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 mr1495 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
vg1009101162 sf1009030023 10 9101162 7.90E-46 5.19E-09
vg0222740991 sf0222735122 2 22740991 6.36E-43 1.03E-11
vg0222732157 sf0222726288 2 22732157 2.19E-42 1.40E-12
vg1009142008 sf1009070869 10 9142008 2.72E-39 2.16E-08
vg0407827227 sf0407822495 4 7827227 7.81E-38 NA
vg1006502151 sf1006517774 10 6502151 1.84E-37 NA
vg1007581951 sf1007597563 10 7581951 1.48E-36 6.97E-12
vg1009172946 sf1009101767 10 9172946 2.57E-34 3.93E-09
vg1009514692 sf1009443513 10 9514692 1.79E-32 NA
vg1216843191 sf1216837145 12 16843191 7.37E-26 4.57E-09
vg0222679274 sf0222673405 2 22679274 3.29E-24 2.35E-17
vg0121803138 sf0121802093 1 21803138 1.29E-23 6.24E-07
vg0220994638 sf0220988770 2 20994638 4.00E-22 NA
vg1007435905 sf1007451528 10 7435905 NA 2.09E-15
vg1009133110 sf1009061971 10 9133110 NA 6.15E-11
vg0407823910 sf0407819178 4 7823910 NA 3.72E-09
vg1007353693 sf1007369316 10 7353693 NA 4.23E-09
vg0616706040 sf0616705042 6 16706040 NA 8.23E-08
vg0106081038 sf0106080038 1 6081038 NA 1.28E-07
vg0223661758 sf0223655889 2 23661758 NA 1.29E-07
vg1005485300 sf1005501837 10 5485300 NA 5.06E-07
vg1110425815 sf1110420360 11 10425815 NA 1.29E-06
vg0223834116 sf0223828247 2 23834116 NA 1.56E-06
vg0140883886 sf0140882843 1 40883886 NA 1.71E-06
vg0222722554 sf0222716685 2 22722554 NA 1.84E-06
vg0204906205 sf0204906202 2 4906205 NA 1.85E-06
vg1016227917 sf1016156689 10 16227917 NA 1.89E-06
vg0316147114 sf0316145761 3 16147114 NA 2.31E-06
vg0500435853 sf0500435853 5 435853 NA 2.32E-06
vg0222725003 sf0222719134 2 22725003 NA 2.48E-06