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 mr1006 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
vg0921461602 sf0921461121 9 21461602 2.50E-23 5.97E-18
vg0921456056 sf0921455575 9 21456056 1.58E-22 1.50E-18
vg1218024420 sf1217995856 12 18024420 1.14E-12 3.00E-06
vg1218024396 sf1217995832 12 18024396 2.61E-12 NA
vg0623497575 sf0623496578 6 23497575 1.02E-11 NA
vg0922446085 sf0922445604 9 22446085 1.69E-11 NA
vg0206385095 sf0206385095 2 6385095 2.50E-11 NA
vg0911617740 sf0911616739 9 11617740 1.50E-07 NA
vg0915096631 sf0915095630 9 15096631 5.16E-06 NA
vg0817164286 sf0817161572 8 17164286 NA 7.58E-07
vg0817029761 sf0817027047 8 17029761 NA 2.88E-06
vg0817111129 sf0817108415 8 17111129 NA 3.61E-06