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 mr1329 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
vg0522383666 sf0522321107 5 22383666 5.12E-16 NA
vg0707469068 sf0707468073 7 7469068 5.32E-16 NA
vg0306023926 sf0306022926 3 6023926 1.41E-15 NA
vg0514329455 sf0514271998 5 14329455 3.94E-15 NA
vg0507010835 sf0507010777 5 7010835 4.92E-15 NA
vg0506979574 sf0506979516 5 6979574 6.78E-15 NA
vg0710222643 sf0710221649 7 10222643 1.26E-14 NA
vg1216930858 sf1216924812 12 16930858 NA 6.59E-07
vg1122543342 sf1122077213 11 22543342 NA 2.95E-06
vg0312663464 sf0312662182 3 12663464 NA 4.63E-06
vg0142482027 sf0142480983 1 42482027 NA 4.69E-06