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 mr1835 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
vg1102232232 sf1102228090 11 2232232 1.49E-18 9.47E-09
vg0407008360 sf0407003631 4 7008360 6.56E-16 NA
vg0410390615 sf0410381314 4 10390615 9.10E-15 NA
vg0231964086 sf0231958217 2 31964086 2.66E-14 NA
vg1207511374 sf1207508780 12 7511374 1.08E-13 1.34E-07
vg0318084743 sf0318083525 3 18084743 NA 2.48E-07
vg0427893228 sf0427708090 4 27893228 NA 2.51E-07
vg1102074001 sf1102069859 11 2074001 NA 5.59E-07
vg0819368604 sf0819365891 8 19368604 NA 8.67E-07
vg0308881162 sf0308880100 3 8881162 NA 2.08E-06
vg0318035297 sf0318034079 3 18035297 NA 2.58E-06
vg0922205633 sf0922205152 9 22205633 NA 2.97E-06
vg0507713423 sf0507713364 5 7713423 NA 3.16E-06
vg0819489414 sf0819486701 8 19489414 NA 3.58E-06
vg0802282522 sf0802281525 8 2282522 NA 3.64E-06
vg1102069789 sf1102065647 11 2069789 NA 4.46E-06
vg0142085781 sf0142084738 1 42085781 NA 4.48E-06
vg0815304114 sf0815301400 8 15304114 NA 5.44E-06