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 mr1618 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
vg0406381089 sf0406376529 4 6381089 4.48E-143 3.31E-30
vg0406526555 sf0406521998 4 6526555 7.42E-143 1.94E-30
vg0406519287 sf0406514730 4 6519287 1.91E-138 2.26E-28
vg1017228554 sf1017157327 10 17228554 2.94E-110 1.11E-08
vg1017223697 sf1017152470 10 17223697 7.93E-110 1.32E-09
vg0411344776 sf0411335479 4 11344776 5.77E-108 NA
vg0305431587 sf0305430587 3 5431587 1.23E-106 NA
vg1012850806 sf1012779621 10 12850806 7.08E-105 5.50E-06
vg1012805563 sf1012734378 10 12805563 8.46E-102 1.93E-06
vg0613777657 sf0613776658 6 13777657 1.58E-96 4.31E-09
vg0613749075 sf0613748076 6 13749075 5.51E-95 5.58E-08
vg0307854597 sf0307853535 3 7854597 1.93E-93 6.05E-07
vg0406521772 sf0406517215 4 6521772 NA 5.83E-11
vg0619806021 sf0619805024 6 19806021 NA 1.15E-08
vg0812764718 sf0812762543 8 12764718 NA 1.97E-08
vg1105930906 sf1105926658 11 5930906 NA 1.99E-08
vg0123735612 sf0123734568 1 23735612 NA 2.20E-08
vg0412088380 sf0412079091 4 12088380 NA 4.64E-08
vg0406344978 sf0406340418 4 6344978 NA 5.21E-08
vg1122650141 sf1122184012 11 22650141 NA 3.87E-07
vg0705963719 sf0705962720 7 5963719 NA 4.41E-07
vg0407576542 sf0407571810 4 7576542 NA 5.61E-07
vg1209905874 sf1209903284 12 9905874 NA 5.75E-07
vg0715849539 sf0715848546 7 15849539 NA 6.61E-07
vg0802884967 sf0802883970 8 2884967 NA 9.11E-07
vg0722597150 sf0722596157 7 22597150 NA 9.88E-07
vg1020743112 sf1020671591 10 20743112 NA 1.08E-06
vg0211839911 sf0211839907 2 11839911 NA 2.46E-06