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 mr1096 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
vg0610566343 sf0610565344 6 10566343 2.88E-57 2.20E-39
vg0610673634 sf0610672635 6 10673634 1.37E-28 4.84E-25
vg0610645429 sf0610644430 6 10645429 1.98E-18 3.53E-11
vg0610626135 sf0610625136 6 10626135 6.69E-18 5.66E-12
vg0610419183 sf0610418184 6 10419183 5.38E-17 4.57E-15
vg0610679932 sf0610678933 6 10679932 1.18E-16 1.41E-18
vg0611098730 sf0611097731 6 11098730 7.19E-16 2.55E-11
vg0610556004 sf0610555005 6 10556004 3.84E-15 7.89E-11
vg0611098317 sf0611097318 6 11098317 1.24E-14 4.21E-11
vg0610873345 sf0610872346 6 10873345 1.39E-14 4.47E-09
vg0610435285 sf0610434286 6 10435285 1.55E-14 1.65E-14
vg0611969595 sf0611968596 6 11969595 9.08E-14 3.00E-07
vg0610609111 sf0610608112 6 10609111 1.06E-12 3.32E-08
vg0610429643 sf0610428644 6 10429643 1.58E-11 3.60E-09
vg0611602553 sf0611601554 6 11602553 2.28E-11 1.50E-08
vg0611654043 sf0611653044 6 11654043 2.52E-11 1.88E-09
vg0610205289 sf0610204290 6 10205289 4.79E-11 6.26E-11
vg0611256787 sf0611255788 6 11256787 6.56E-11 1.77E-09
vg0610119475 sf0610118476 6 10119475 8.33E-11 3.87E-11
vg0611004237 sf0611003238 6 11004237 1.38E-09 3.30E-09
vg0610873253 sf0610872254 6 10873253 1.62E-07 7.88E-12
vg0610752378 sf0610751379 6 10752378 1.84E-07 1.53E-08
vg0805587944 sf0805586947 8 5587944 1.39E-06 2.26E-07
vg0618988041 sf0618987044 6 18988041 1.53E-06 4.64E-09
vg0222739831 sf0222733962 2 22739831 NA 1.35E-09
vg0222722590 sf0222716721 2 22722590 NA 2.62E-06
vg0807847137 sf0807846141 8 7847137 NA 8.06E-06