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 mr1732 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
vg1217808832 sf1217780266 12 17808832 8.50E-09 2.75E-07
vg1125509643 sf1125043482 11 25509643 8.59E-09 2.39E-08
vg1125470848 sf1125004687 11 25470848 9.92E-09 2.03E-08
vg0713262354 sf0713261361 7 13262354 9.21E-08 2.96E-07
vg1200849729 sf1200848729 12 849729 1.07E-07 3.65E-06
vg1126213378 sf1125741792 11 26213378 1.65E-07 1.54E-06
vg0104008756 sf0104007756 1 4008756 2.94E-07 2.60E-07
vg1214707367 sf1214704708 12 14707367 5.47E-07 2.16E-06
vg0921839494 sf0921839013 9 21839494 7.01E-07 3.63E-06
vg1218108461 sf1218079897 12 18108461 1.20E-06 1.33E-06
vg1005112746 sf1005129283 10 5112746 1.89E-06 1.30E-06
vg0211327689 sf0211327686 2 11327689 2.62E-06 2.39E-06
vg0819321720 sf0819319007 8 19321720 3.87E-06 1.97E-06
vg0103998281 sf0103997281 1 3998281 5.47E-06 2.93E-06
vg0122690936 sf0122689891 1 22690936 6.09E-06 8.24E-07
vg0917631772 sf0917630771 9 17631772 NA 2.40E-06