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 mr1856 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
vg1214111586 sf1214108926 12 14111586 1.42E-08 1.43E-08
vg0522014819 sf0521952261 5 22014819 5.59E-08 5.62E-08
vg1213935504 sf1213932842 12 13935504 1.07E-07 1.08E-07
vg0125127326 sf0125126282 1 25127326 3.68E-07 3.70E-07
vg0800190791 sf0800189791 8 190791 1.25E-06 1.26E-06
vg1211108486 sf1211105850 12 11108486 1.30E-06 1.31E-06
vg1210657344 sf1210654757 12 10657344 1.60E-06 1.61E-06
vg1218117927 sf1218089363 12 18117927 3.59E-06 3.59E-06
vg1204021683 sf1204020671 12 4021683 3.98E-06 4.00E-06
vg0134125967 sf0134124923 1 34125967 4.34E-06 4.36E-06
vg0125070140 sf0125069096 1 25070140 4.83E-06 4.83E-06