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 mr1452 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
vg0141773367 sf0141772324 1 41773367 5.30E-09 NA
vg0306401421 sf0306400421 3 6401421 8.69E-09 NA
vg0524787051 sf0524724466 5 24787051 1.06E-08 NA
vg0210856039 sf0210856037 2 10856039 1.76E-08 NA
vg0916032111 sf0916031110 9 16032111 1.77E-08 6.41E-06
vg0503080037 sf0503080013 5 3080037 1.30E-07 3.19E-06
vg0107647091 sf0107646091 1 7647091 2.40E-07 3.53E-07
vg0524514817 sf0524452238 5 24514817 8.10E-07 NA
vg0804887405 sf0804886408 8 4887405 3.35E-06 6.59E-06
vg0630306971 sf0630305973 6 30306971 3.60E-06 4.14E-06
vg0709128655 sf0709127661 7 9128655 7.99E-06 3.85E-06