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 mr1698 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
vg1000933071 sf1000932047 10 933071 1.02E-09 7.36E-07
vg0403778987 sf0403774592 4 3778987 1.04E-09 9.93E-07
vg1121468317 sf1121002194 11 21468317 2.02E-09 4.96E-07
vg1000936710 sf1000935686 10 936710 6.79E-09 2.29E-07
vg1127835781 sf1127364167 11 27835781 1.04E-08 4.29E-06
vg1015191238 sf1015120006 10 15191238 1.86E-08 2.29E-06
vg1128863871 sf1128340650 11 28863871 2.34E-08 1.22E-06
vg1015051125 sf1014979891 10 15051125 3.60E-08 4.64E-07
vg1000028798 sf1000027798 10 28798 1.61E-07 1.92E-06
vg1222438799 sf1222405238 12 22438799 2.93E-07 2.40E-06
vg0413844880 sf0413835598 4 13844880 4.10E-07 3.30E-06
vg0904236778 sf0904235778 9 4236778 2.27E-06 3.01E-06
vg0620513238 sf0620512241 6 20513238 6.29E-06 3.24E-06