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 mr1518 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
vg0919848647 sf0919848166 9 19848647 1.04E-18 2.72E-11
vg0920162123 sf0920161642 9 20162123 5.71E-15 1.70E-11
vg0217328110 sf0217322240 2 17328110 2.74E-10 7.66E-07
vg0117784588 sf0117783542 1 17784588 3.26E-10 NA
vg1217519399 sf1217513354 12 17519399 3.94E-10 NA
vg1219154558 sf1219125992 12 19154558 5.05E-10 5.88E-06
vg0305233552 sf0305232552 3 5233552 6.81E-10 9.59E-07
vg0107036111 sf0107035111 1 7036111 4.69E-08 1.65E-06
vg0715448729 sf0715447736 7 15448729 9.03E-08 1.38E-06
vg0608650180 sf0608649181 6 8650180 1.30E-07 4.04E-06
vg0117128761 sf0117127715 1 17128761 1.95E-06 NA
vg0512238377 sf0512238307 5 12238377 NA 2.73E-06