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 mr1822 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
vg0623981969 sf0623980972 6 23981969 1.31E-07 1.31E-07
vg0421384856 sf0421212909 4 21384856 3.11E-07 3.11E-07
vg0421454162 sf0421282213 4 21454162 5.59E-07 5.59E-07
vg0607659813 sf0607658814 6 7659813 6.67E-07 6.67E-07
vg0727868341 sf0727867348 7 27868341 1.22E-06 1.22E-06
vg0420711795 sf0420539838 4 20711795 1.52E-06 1.52E-06
vg0921004343 sf0921003862 9 21004343 1.67E-06 1.67E-06
vg0521872068 sf0521809510 5 21872068 3.31E-06 3.31E-06
vg0424181194 sf0423996055 4 24181194 3.41E-06 3.41E-06
vg0805826839 sf0805825842 8 5826839 4.20E-06 4.20E-06
vg1104467562 sf1104463464 11 4467562 4.24E-06 4.24E-06
vg0904149706 sf0904148706 9 4149706 4.62E-06 4.62E-06