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 mr1218 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
vg0610558103 sf0610557104 6 10558103 5.26E-32 1.23E-15
vg0610608095 sf0610607096 6 10608095 1.51E-29 7.80E-16
vg0610075227 sf0610074228 6 10075227 3.95E-27 5.10E-13
vg0610027827 sf0610026828 6 10027827 2.79E-19 6.70E-09
vg0617359224 sf0617358227 6 17359224 1.05E-17 NA
vg0609676503 sf0609675504 6 9676503 1.04E-16 4.26E-07
vg0610371509 sf0610370510 6 10371509 5.66E-16 1.28E-11
vg0610273791 sf0610272792 6 10273791 8.27E-15 1.05E-08
vg0610445215 sf0610444216 6 10445215 7.30E-13 7.23E-09
vg0611962313 sf0611961314 6 11962313 1.95E-11 3.16E-06
vg0616894133 sf0616893136 6 16894133 2.44E-10 3.69E-06
vg0610366774 sf0610365775 6 10366774 4.91E-10 1.37E-10
vg0610061410 sf0610060411 6 10061410 9.33E-10 8.04E-08
vg0610955362 sf0610954363 6 10955362 1.52E-09 1.78E-08
vg0611007112 sf0611006113 6 11007112 4.19E-08 1.89E-08
vg0610590324 sf0610589325 6 10590324 6.68E-08 1.53E-06
vg0600576807 sf0600575808 6 576807 NA 1.79E-06
vg0609445027 sf0609444028 6 9445027 NA 4.54E-06