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 mr1203 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
vg0406526555 sf0406521998 4 6526555 4.10E-148 1.85E-30
vg1017228554 sf1017157327 10 17228554 1.66E-111 1.44E-07
vg0305431587 sf0305430587 3 5431587 1.75E-111 NA
vg0411344776 sf0411335479 4 11344776 6.50E-111 NA
vg1017223697 sf1017152470 10 17223697 1.45E-110 2.82E-08
vg0621000047 sf0620999050 6 21000047 3.59E-109 NA
vg0822651774 sf0822649061 8 22651774 3.19E-102 4.12E-06
vg0613777657 sf0613776658 6 13777657 9.65E-101 8.31E-10
vg0807117547 sf0807116552 8 7117547 6.35E-98 1.04E-06
vg0619719272 sf0619718275 6 19719272 1.03E-95 2.45E-11
vg0307854597 sf0307853535 3 7854597 2.44E-95 1.08E-06
vg0711095110 sf0711094116 7 11095110 3.80E-95 7.78E-07
vg0406521772 sf0406517215 4 6521772 NA 9.02E-11
vg0619681988 sf0619680991 6 19681988 NA 8.37E-10
vg0415203123 sf0415193838 4 15203123 NA 2.69E-08
vg0619679605 sf0619678608 6 19679605 NA 3.28E-08
vg0411635497 sf0411626203 4 11635497 NA 6.06E-08
vg0407576542 sf0407571810 4 7576542 NA 1.55E-07
vg0720714007 sf0720713014 7 20714007 NA 1.91E-07
vg0713947405 sf0713946412 7 13947405 NA 2.16E-07
vg1105930906 sf1105926658 11 5930906 NA 2.38E-07
vg1209907443 sf1209904853 12 9907443 NA 2.43E-07
vg0619861955 sf0619860958 6 19861955 NA 3.13E-07
vg1122664014 sf1122197885 11 22664014 NA 3.49E-07
vg0406345405 sf0406340845 4 6345405 NA 3.92E-07
vg0722665343 sf0722664350 7 22665343 NA 4.62E-07
vg1204022316 sf1204021304 12 4022316 NA 5.84E-07
vg0613730159 sf0613729160 6 13730159 NA 6.79E-07
vg0123735612 sf0123734568 1 23735612 NA 8.92E-07
vg0614300581 sf0614299582 6 14300581 NA 1.81E-06
vg0715307926 sf0715306933 7 15307926 NA 4.96E-06