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 mr1489 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
vg1215869969 sf1215867265 12 15869969 1.27E-42 1.96E-21
vg1211103816 sf1211101182 12 11103816 9.73E-18 NA
vg0218132013 sf0218126144 2 18132013 8.12E-16 5.26E-07
vg0724570350 sf0724569356 7 24570350 1.71E-15 NA
vg0919147683 sf0919147272 9 19147683 8.55E-15 NA
vg1216138955 sf1216136251 12 16138955 NA 8.61E-09
vg0901048761 sf0901047761 9 1048761 NA 8.93E-08
vg0610620315 sf0610619316 6 10620315 NA 1.56E-06
vg0317414701 sf0317413511 3 17414701 NA 1.95E-06
vg1216017848 sf1216015144 12 16017848 NA 4.20E-06