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 mr1164 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
vg0103418043 sf0103417043 1 3418043 3.50E-20 NA
vg0910353994 sf0910352993 9 10353994 4.57E-19 NA
vg0103143509 sf0103142509 1 3143509 7.83E-19 1.80E-06
vg0228634958 sf0228629089 2 28634958 4.59E-18 NA
vg0423891208 sf0423706066 4 23891208 4.62E-18 NA
vg0419784082 sf0419612119 4 19784082 5.08E-18 NA
vg0910454036 sf0910453035 9 10454036 2.41E-17 2.64E-06
vg0910161376 sf0910160375 9 10161376 3.76E-16 NA
vg0402311534 sf0402307129 4 2311534 NA 2.74E-08
vg0710293172 sf0710292178 7 10293172 NA 5.62E-07
vg0410398025 sf0410388724 4 10398025 NA 7.66E-07
vg0305100673 sf0305099675 3 5100673 NA 8.45E-07
vg1116232716 sf1115767586 11 16232716 NA 9.47E-07
vg0115915963 sf0115914937 1 15915963 NA 1.15E-06
vg0711574253 sf0711573259 7 11574253 NA 1.71E-06
vg0617335611 sf0617334614 6 17335611 NA 2.11E-06
vg0621649782 sf0621648785 6 21649782 NA 2.43E-06
vg1211846648 sf1211843984 12 11846648 NA 2.43E-06
vg0425861893 sf0425676761 4 25861893 NA 2.50E-06
vg1127372013 sf1126900400 11 27372013 NA 2.71E-06
vg1203784794 sf1203783793 12 3784794 NA 2.78E-06
vg0813870955 sf0813868241 8 13870955 NA 2.83E-06
vg0207239229 sf0207239229 2 7239229 NA 3.41E-06
vg1017498974 sf1017427747 10 17498974 NA 4.60E-06
vg0222538877 sf0222533008 2 22538877 NA 7.52E-06