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 mr1389 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
vg0140121196 sf0140120153 1 40121196 4.19E-10 4.19E-10
vg0627957904 sf0627956906 6 27957904 2.07E-08 2.07E-08
vg0906217253 sf0906216253 9 6217253 2.43E-08 2.43E-08
vg0430744138 sf0430559010 4 30744138 3.56E-08 3.56E-08
vg1203799300 sf1203798299 12 3799300 4.15E-08 4.15E-08
vg0906091731 sf0906090731 9 6091731 5.53E-08 5.53E-08
vg0708383438 sf0708382443 7 8383438 9.84E-08 9.84E-08
vg0603087867 sf0603086868 6 3087867 1.02E-07 1.02E-07
vg0822997346 sf0822994633 8 22997346 1.17E-07 1.17E-07
vg0906656639 sf0906655639 9 6656639 1.20E-07 1.20E-07
vg0819069416 sf0819066703 8 19069416 1.62E-07 1.62E-07
vg0711311644 sf0711310650 7 11311644 2.02E-07 2.02E-07
vg0816355374 sf0816352660 8 16355374 2.48E-07 2.48E-07
vg0615688331 sf0615687333 6 15688331 2.83E-07 2.83E-07
vg0221522352 sf0221516483 2 21522352 2.86E-07 2.86E-07
vg1000250476 sf1000249476 10 250476 3.07E-07 3.07E-07
vg0310342563 sf0310341479 3 10342563 3.68E-07 3.68E-07
vg0106088288 sf0106087288 1 6088288 5.02E-07 5.02E-07
vg0233356353 sf0233350484 2 33356353 5.08E-07 5.08E-07
vg0906202716 sf0906201716 9 6202716 5.24E-07 5.23E-07
vg0711014575 sf0711013581 7 11014575 5.26E-07 5.26E-07