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 mr1080 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 1.51E-119 2.34E-22
vg1016650869 sf1016579642 10 16650869 8.79E-93 2.08E-06
vg0122833397 sf0122832353 1 22833397 1.38E-92 NA
vg0411344776 sf0411335479 4 11344776 3.95E-92 NA
vg1016528662 sf1016457435 10 16528662 6.19E-91 2.19E-07
vg0305431587 sf0305430587 3 5431587 1.40E-89 NA
vg0704679864 sf0704678865 7 4679864 1.55E-89 8.17E-07
vg0617167421 sf0617166424 6 17167421 3.84E-89 2.10E-06
vg0613777657 sf0613776658 6 13777657 4.11E-86 6.71E-09
vg0412479470 sf0412470185 4 12479470 1.39E-84 2.89E-07
vg0406521772 sf0406517215 4 6521772 NA 1.80E-08
vg0715849539 sf0715848546 7 15849539 NA 2.68E-08
vg0817943383 sf0817940670 8 17943383 NA 4.01E-08
vg0123800969 sf0123799925 1 23800969 NA 1.55E-07
vg0619733305 sf0619732308 6 19733305 NA 4.78E-07
vg0704572014 sf0704571015 7 4572014 NA 5.56E-07
vg1209905874 sf1209903284 12 9905874 NA 6.50E-07
vg0613730159 sf0613729160 6 13730159 NA 1.48E-06
vg0814055215 sf0814052501 8 14055215 NA 1.51E-06
vg0411637990 sf0411628696 4 11637990 NA 1.89E-06
vg0820868579 sf0820865866 8 20868579 NA 2.07E-06
vg1209714251 sf1209711660 12 9714251 NA 2.17E-06
vg0817943381 sf0817940668 8 17943381 NA 2.20E-06
vg0521967722 sf0521905164 5 21967722 NA 2.32E-06
vg0407576542 sf0407571810 4 7576542 NA 3.21E-06
vg0817306917 sf0817304203 8 17306917 NA 3.49E-06
vg0806964414 sf0806963419 8 6964414 NA 4.77E-06
vg0222742146 sf0222736277 2 22742146 NA 8.03E-06