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
vg0120297000 sf0120295955 1 20297000 1.35E-11 1.35E-11
vg0906217253 sf0906216253 9 6217253 2.27E-11 2.27E-11
vg0221522352 sf0221516483 2 21522352 2.95E-11 2.95E-11
vg0117419683 sf0117418637 1 17419683 9.40E-11 9.40E-11
vg0906091731 sf0906090731 9 6091731 4.16E-10 4.16E-10
vg1000256952 sf1000255952 10 256952 7.63E-10 7.63E-10
vg0729253239 sf0729252247 7 29253239 1.87E-09 1.87E-09
vg0708154795 sf0708153800 7 8154795 2.42E-09 2.42E-09
vg0819130178 sf0819127465 8 19130178 2.58E-09 2.58E-09
vg0901039207 sf0901038207 9 1039207 2.87E-09 2.87E-09
vg1127077047 sf1126605434 11 27077047 3.40E-09 3.40E-09
vg0708450949 sf0708449954 7 8450949 4.52E-09 4.52E-09
vg1013678979 sf1013607748 10 13678979 5.93E-09 5.93E-09
vg0500885332 sf0500885314 5 885332 6.45E-09 6.45E-09
vg0915861397 sf0915860396 9 15861397 7.30E-09 7.30E-09
vg0219891676 sf0219885808 2 19891676 8.96E-09 8.96E-09
vg0906358576 sf0906357576 9 6358576 2.03E-08 2.03E-08
vg0708820220 sf0708819225 7 8820220 2.59E-08 2.59E-08
vg0912682054 sf0912681053 9 12682054 6.05E-08 6.05E-08
vg0233808913 sf0233803044 2 33808913 6.14E-08 6.14E-08