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 mr1119 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
vg1009129498 sf1009058359 10 9129498 9.00E-15 2.83E-08
vg1008520987 sf1008449849 10 8520987 1.15E-14 6.28E-10
vg1006490817 sf1006506440 10 6490817 4.33E-14 2.16E-08
vg1204314449 sf1204313437 12 4314449 3.20E-12 2.84E-08
vg0407822984 sf0407818252 4 7822984 1.76E-11 8.84E-07
vg1005923799 sf1005940337 10 5923799 3.41E-11 1.76E-07
vg1216843191 sf1216837145 12 16843191 1.45E-10 8.12E-07
vg0335354580 sf0335347449 3 35354580 2.45E-08 2.16E-07
vg0501908149 sf0501908131 5 1908149 2.70E-08 4.39E-07
vg0403205910 sf0403201513 4 3205910 3.77E-08 2.94E-07
vg0619894434 sf0619893437 6 19894434 6.34E-08 4.43E-06
vg0708595948 sf0708594953 7 8595948 1.22E-07 4.50E-06
vg0504710532 sf0504710509 5 4710532 2.73E-07 2.88E-06
vg0334655144 sf0334648014 3 34655144 3.05E-07 1.84E-06
vg1006726777 sf1006742400 10 6726777 2.02E-06 2.57E-06
vg1121793608 sf1121327485 11 21793608 3.14E-06 NA
vg0335766999 sf0335759868 3 35766999 3.20E-06 4.59E-07
vg0402649523 sf0402645127 4 2649523 3.97E-06 2.36E-06
vg0504428872 sf0504428849 5 4428872 8.88E-06 NA
vg0417689977 sf0417518018 4 17689977 NA 1.01E-06
vg1113389475 sf1112925796 11 13389475 NA 4.12E-06
vg0403136466 sf0403132069 4 3136466 NA 4.47E-06
vg1116002197 sf1115537069 11 16002197 NA 4.49E-06
vg0334746454 sf0334739324 3 34746454 NA 5.00E-06
vg0516073587 sf0516016071 5 16073587 NA 5.35E-06
vg1020189984 sf1020118466 10 20189984 NA 9.47E-06