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 mr1916 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
vg0106836437 sf0106835437 1 6836437 1.07E-31 2.19E-09
vg0106731782 sf0106730782 1 6731782 2.07E-29 4.23E-18
vg0117983878 sf0117982832 1 17983878 1.30E-28 NA
vg0106688727 sf0106687727 1 6688727 1.37E-28 4.01E-18
vg0428455216 sf0428270069 4 28455216 3.18E-28 NA
vg0407379220 sf0407374489 4 7379220 6.71E-28 NA
vg0827125579 sf0827122865 8 27125579 1.76E-25 2.43E-07
vg0805970126 sf0805969129 8 5970126 3.02E-25 8.98E-09
vg0420209955 sf0420038000 4 20209955 3.97E-24 NA
vg0105808299 sf0105807299 1 5808299 NA 7.22E-09
vg0107074175 sf0107073175 1 7074175 NA 1.44E-07
vg0822330414 sf0822327701 8 22330414 NA 1.77E-07
vg1214656787 sf1214654127 12 14656787 NA 3.99E-07
vg0310483495 sf0310482411 3 10483495 NA 4.01E-07
vg0915957092 sf0915956091 9 15957092 NA 6.18E-07
vg0800333217 sf0800332217 8 333217 NA 9.39E-07
vg0106685208 sf0106684208 1 6685208 NA 1.00E-06
vg1115925850 sf1115460720 11 15925850 NA 1.15E-06
vg0716837850 sf0716836857 7 16837850 NA 1.80E-06
vg0816444910 sf0816442196 8 16444910 NA 3.70E-06
vg0921539163 sf0921538682 9 21539163 NA 3.95E-06
vg1214356031 sf1214353371 12 14356031 NA 4.13E-06