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 mr1348 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
vg1110064581 sf1110059158 11 10064581 2.76E-12 NA
vg1223453994 sf1223420454 12 23453994 6.44E-12 NA
vg0611702154 sf0611701155 6 11702154 1.00E-11 NA
vg0827469774 sf0827467060 8 27469774 1.07E-11 NA
vg0627565709 sf0627564711 6 27565709 1.22E-11 NA
vg0817313550 sf0817310836 8 17313550 NA 1.50E-06
vg0612239920 sf0612238921 6 12239920 NA 2.50E-06
vg1201779595 sf1201778592 12 1779595 NA 4.12E-06
vg0727660294 sf0727659301 7 27660294 NA 5.10E-06