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 mr1155 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
vg0719051105 sf0719050112 7 19051105 4.60E-38 1.33E-22
vg0719051163 sf0719050170 7 19051163 4.31E-37 8.59E-23
vg0719317459 sf0719316466 7 19317459 1.01E-15 5.25E-09
vg0719300893 sf0719299900 7 19300893 2.41E-15 1.24E-09
vg0123892965 sf0123891921 1 23892965 3.48E-13 NA
vg0725365363 sf0725364369 7 25365363 4.70E-13 8.12E-06
vg0707768545 sf0707767550 7 7768545 7.07E-13 8.08E-09
vg0718994201 sf0718993208 7 18994201 8.15E-13 1.68E-08
vg0715949888 sf0715948895 7 15949888 1.99E-12 3.19E-08
vg0718984454 sf0718983461 7 18984454 7.18E-10 5.89E-08
vg1207863655 sf1207861061 12 7863655 1.15E-09 2.01E-08
vg0718983067 sf0718982074 7 18983067 2.76E-09 3.53E-06
vg0226057933 sf0226052064 2 26057933 5.34E-09 1.18E-07
vg1218104899 sf1218076335 12 18104899 1.07E-08 1.35E-06
vg0719140489 sf0719139496 7 19140489 3.88E-08 3.11E-06
vg0504617447 sf0504617424 5 4617447 1.39E-07 1.18E-06
vg0401257635 sf0401253185 4 1257635 2.30E-06 NA
vg0622747039 sf0622746042 6 22747039 2.88E-06 NA
vg0915181272 sf0915180271 9 15181272 NA 1.49E-08
vg1109955379 sf1109949956 11 9955379 NA 2.68E-06