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 mr1567 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
vg1221084756 sf1221051306 12 21084756 1.02E-10 9.12E-09
vg1221050837 sf1221017387 12 21050837 3.02E-10 1.84E-07
vg1221086538 sf1221053088 12 21086538 1.82E-09 3.17E-08
vg0807470228 sf0807469233 8 7470228 2.27E-09 2.03E-08
vg0517176749 sf0517116390 5 17176749 3.56E-09 2.77E-06
vg0518099801 sf0518039287 5 18099801 4.50E-09 2.32E-06
vg1220865088 sf1220831637 12 20865088 1.37E-08 3.28E-07
vg0807909279 sf0807908283 8 7909279 3.10E-08 1.26E-06
vg0805916766 sf0805915769 8 5916766 3.95E-08 4.33E-07
vg0300503911 sf0300502909 3 503911 4.55E-08 2.59E-06
vg1220299776 sf1220271218 12 20299776 6.60E-08 2.20E-06
vg1214823188 sf1214820529 12 14823188 8.06E-08 2.79E-07
vg1021307711 sf1021236189 10 21307711 8.51E-08 2.29E-06
vg0321862328 sf0321860838 3 21862328 3.97E-07 4.42E-06
vg0806548377 sf0806547382 8 6548377 8.17E-07 3.33E-06
vg0315981787 sf0315980434 3 15981787 1.01E-06 4.64E-07
vg0207269822 sf0207269822 2 7269822 2.16E-06 3.72E-06
vg1209700563 sf1209697972 12 9700563 2.52E-06 4.17E-06
vg0208339463 sf0208339462 2 8339463 4.67E-06 4.55E-06
vg0207321345 sf0207321345 2 7321345 6.12E-06 NA