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 mr1204 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
vg0719058961 sf0719057968 7 19058961 2.17E-13 2.17E-13
vg0719057997 sf0719057004 7 19057997 8.36E-11 8.35E-11
vg0719049384 sf0719048391 7 19049384 1.51E-10 1.51E-10
vg0719139937 sf0719138944 7 19139937 1.79E-09 1.79E-09
vg0107168392 sf0107167392 1 7168392 2.17E-09 2.17E-09
vg1100694812 sf1100693815 11 694812 3.87E-08 3.87E-08
vg0602363435 sf0602362436 6 2363435 5.79E-08 5.79E-08
vg0811122650 sf0811121655 8 11122650 8.73E-08 8.73E-08
vg0516162890 sf0516105374 5 16162890 1.13E-07 1.13E-07
vg0328527072 sf0328520125 3 28527072 1.25E-07 1.25E-07
vg1020494793 sf1020423272 10 20494793 1.74E-07 1.74E-07
vg0714207090 sf0714206097 7 14207090 2.38E-07 2.37E-07
vg0417642687 sf0417470728 4 17642687 3.30E-07 3.30E-07
vg1017997693 sf1017926465 10 17997693 3.60E-07 3.60E-07
vg0802074891 sf0802073894 8 2074891 3.93E-07 3.93E-07
vg0208176132 sf0208176131 2 8176132 4.04E-07 4.04E-07
vg0708134630 sf0708133635 7 8134630 4.23E-07 4.23E-07
vg1213429246 sf1213426584 12 13429246 5.10E-07 5.10E-07
vg0729311768 sf0729310776 7 29311768 5.53E-07 5.53E-07
vg1125341795 sf1124875635 11 25341795 6.66E-07 6.66E-07
vg1216282451 sf1216279747 12 16282451 7.53E-07 7.53E-07
vg0700559381 sf0700558381 7 559381 7.92E-07 7.92E-07