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 mr1820 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
vg0123690615 sf0123689571 1 23690615 2.75E-09 NA
vg0726964336 sf0726963342 7 26964336 3.33E-09 NA
vg0130163180 sf0130162135 1 30163180 2.75E-08 NA
vg0821970212 sf0821967499 8 21970212 4.36E-08 NA
vg0125460828 sf0125459784 1 25460828 5.29E-08 NA
vg1106375766 sf1106371518 11 6375766 1.82E-06 8.41E-07
vg1128443567 sf1127920346 11 28443567 7.38E-06 NA
vg0210809501 sf0210809499 2 10809501 7.62E-06 NA