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 mr1078 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
vg0610566709 sf0610565710 6 10566709 2.63E-42 4.95E-26
vg0417039665 sf0416867707 4 17039665 4.50E-16 1.34E-07
vg0610583955 sf0610582956 6 10583955 1.66E-15 1.55E-09
vg0920307704 sf0920307223 9 20307704 7.64E-15 9.24E-07
vg0617319066 sf0617318069 6 17319066 1.77E-14 3.63E-07
vg0610428814 sf0610427815 6 10428814 1.59E-13 2.24E-10
vg0610323245 sf0610322246 6 10323245 1.02E-12 5.31E-12
vg0611736174 sf0611735175 6 11736174 1.93E-12 2.27E-07
vg0421446404 sf0421274455 4 21446404 2.44E-12 1.26E-07
vg0612051676 sf0612050677 6 12051676 9.95E-12 3.97E-08
vg0613062563 sf0613061564 6 13062563 3.24E-10 3.41E-07
vg0610462854 sf0610461855 6 10462854 3.38E-10 3.28E-07
vg0610211069 sf0610210070 6 10211069 1.35E-09 8.97E-07
vg0611326373 sf0611325374 6 11326373 2.55E-09 9.23E-07
vg0617636590 sf0617635593 6 17636590 3.11E-09 8.61E-07
vg0610393322 sf0610392323 6 10393322 8.95E-09 1.62E-08
vg0630077328 sf0630076330 6 30077328 1.66E-08 1.04E-06
vg0610119083 sf0610118084 6 10119083 2.38E-08 4.17E-09
vg0610556004 sf0610555005 6 10556004 3.05E-08 4.54E-08
vg0611096080 sf0611095081 6 11096080 1.19E-07 4.87E-07
vg1115480616 sf1115016929 11 15480616 NA 3.92E-07
vg0121366875 sf0121365830 1 21366875 NA 6.57E-06