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 mr1991 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
vg1208270538 sf1208267943 12 8270538 3.21E-07 3.21E-07
vg0300330721 sf0300329719 3 330721 1.38E-06 1.38E-06
vg0520492483 sf0520429954 5 20492483 2.24E-06 2.24E-06
vg0514763041 sf0514705584 5 14763041 2.44E-06 2.44E-06
vg0910979875 sf0910978874 9 10979875 3.73E-06 3.73E-06
vg1122448541 sf1121982412 11 22448541 3.86E-06 3.86E-06
vg0629854146 sf0629853148 6 29854146 4.02E-06 4.02E-06
vg0907413545 sf0907412545 9 7413545 5.29E-06 5.29E-06
vg1220340557 sf1220311999 12 20340557 7.76E-06 7.76E-06