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 mr1801 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
vg1218054911 sf1218026347 12 18054911 5.45E-12 3.00E-07
vg0111928641 sf0111927615 1 11928641 5.21E-11 1.79E-06
vg0330107231 sf0330100270 3 30107231 2.20E-10 3.14E-06
vg0135794714 sf0135793671 1 35794714 4.72E-10 NA
vg1002090281 sf1002089258 10 2090281 5.33E-10 NA
vg0140997622 sf0140996579 1 40997622 1.54E-08 1.02E-06
vg1009009289 sf1008938150 10 9009289 NA 1.55E-06
vg0123950642 sf0123949598 1 23950642 NA 1.75E-06
vg0706378896 sf0706377901 7 6378896 NA 1.95E-06
vg1127725153 sf1127253539 11 27725153 NA 2.62E-06