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 mr1732 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
vg1125222805 sf1124756645 11 25222805 6.22E-24 NA
vg1216359627 sf1216356923 12 16359627 9.73E-24 NA
vg0516005213 sf0515947721 5 16005213 1.80E-23 NA
vg0804724763 sf0804723766 8 4724763 6.72E-23 NA
vg1019048612 sf1018977169 10 19048612 4.38E-22 NA
vg1217053914 sf1217047868 12 17053914 4.53E-21 1.15E-07
vg1016195699 sf1016124471 10 16195699 7.39E-19 1.79E-06
vg0129866460 sf0129865415 1 29866460 NA 1.49E-08
vg1115373505 sf1114909819 11 15373505 NA 1.68E-07
vg0726876447 sf0726875453 7 26876447 NA 6.11E-07
vg1208270520 sf1208267925 12 8270520 NA 9.11E-07
vg0918838703 sf0918837703 9 18838703 NA 2.11E-06
vg1208123893 sf1208121299 12 8123893 NA 3.11E-06
vg0107647091 sf0107646091 1 7647091 NA 3.96E-06
vg1218416620 sf1218388056 12 18416620 NA 4.37E-06
vg0827033027 sf0827030313 8 27033027 NA 6.34E-06
vg1218417268 sf1218388704 12 18417268 NA 7.35E-06