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 mr1870 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
vg0721303275 sf0721302282 7 21303275 2.18E-21 NA
vg1107883533 sf1107879278 11 7883533 5.02E-21 NA
vg0121993603 sf0121992558 1 21993603 2.89E-20 NA
vg0503689343 sf0503689320 5 3689343 4.95E-20 NA
vg0100448187 sf0100447187 1 448187 9.03E-20 NA
vg0207449651 sf0207449651 2 7449651 2.63E-17 NA
vg0921458072 sf0921457591 9 21458072 NA 4.11E-07
vg0504616802 sf0504616779 5 4616802 NA 3.01E-06
vg0529077142 sf0529014497 5 29077142 NA 3.62E-06
vg1105587916 sf1105583668 11 5587916 NA 9.07E-06