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 mr1178 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
vg1215956495 sf1215953791 12 15956495 2.86E-57 6.28E-28
vg1215955784 sf1215953080 12 15955784 5.72E-57 6.13E-28
vg1011512136 sf1011440955 10 11512136 1.35E-22 3.24E-07
vg1011511779 sf1011440598 10 11511779 1.78E-22 1.62E-07
vg0500829493 sf0500829475 5 829493 1.11E-20 NA
vg1212873997 sf1212871336 12 12873997 2.04E-20 8.11E-08
vg0821312081 sf0821309368 8 21312081 6.88E-19 NA
vg0919099872 sf0919099461 9 19099872 2.52E-17 3.80E-06
vg1018570337 sf1018498894 10 18570337 6.07E-17 2.89E-06
vg0229534325 sf0229528456 2 29534325 1.33E-15 4.86E-06
vg1204499186 sf1204498174 12 4499186 1.24E-13 1.17E-06
vg1215852700 sf1215849996 12 15852700 NA 4.48E-10
vg1022588644 sf1022517118 10 22588644 NA 2.41E-09
vg1216347683 sf1216344979 12 16347683 NA 1.02E-08
vg0901555680 sf0901554680 9 1555680 NA 1.32E-07
vg1212876949 sf1212874288 12 12876949 NA 1.37E-07
vg1006587700 sf1006603323 10 6587700 NA 6.31E-07
vg1215670841 sf1215668138 12 15670841 NA 1.16E-06
vg1213186520 sf1213183858 12 13186520 NA 1.79E-06
vg0623791757 sf0623790760 6 23791757 NA 4.03E-06
vg1121619953 sf1121153830 11 21619953 NA 4.70E-06