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 mr1954 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
vg0725435511 sf0725434517 7 25435511 1.10E-07 1.11E-07
vg1207043060 sf1207041950 12 7043060 4.03E-07 4.05E-07
vg0805698451 sf0805697454 8 5698451 6.41E-07 6.45E-07
vg0330841392 sf0330834279 3 30841392 6.71E-07 6.75E-07
vg0500821426 sf0500821408 5 821426 1.10E-06 1.10E-06
vg0103290887 sf0103289887 1 3290887 1.49E-06 1.50E-06
vg0800185506 sf0800184506 8 185506 1.57E-06 1.58E-06
vg0416147172 sf0415975205 4 16147172 2.09E-06 2.10E-06
vg1001445274 sf1001444251 10 1445274 2.32E-06 2.33E-06
vg1218320965 sf1218292401 12 18320965 2.83E-06 2.85E-06
vg0218747822 sf0218741953 2 18747822 3.08E-06 3.09E-06
vg1206348060 sf1206346950 12 6348060 3.23E-06 3.25E-06
vg0410490234 sf0410480933 4 10490234 3.52E-06 3.54E-06
vg0912645942 sf0912644941 9 12645942 4.24E-06 4.27E-06
vg0916425614 sf0916424613 9 16425614 4.40E-06 4.43E-06