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 mr1286 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
vg0726559146 sf0726558152 7 26559146 1.88E-08 1.88E-08
vg0430475778 sf0430290656 4 30475778 2.52E-07 2.53E-07
vg0102103204 sf0102102204 1 2103204 3.34E-07 3.34E-07
vg0606329912 sf0606328913 6 6329912 3.47E-07 3.48E-07
vg0805992743 sf0805991746 8 5992743 3.78E-07 3.79E-07
vg0142427760 sf0142426716 1 42427760 4.33E-07 4.34E-07
vg0223525077 sf0223519208 2 23525077 5.30E-07 5.30E-07
vg1020531763 sf1020460242 10 20531763 6.65E-07 6.66E-07
vg0217104494 sf0217098624 2 17104494 7.78E-07 7.80E-07
vg1117997316 sf1117531174 11 17997316 7.87E-07 7.89E-07
vg0801697883 sf0801696886 8 1697883 1.03E-06 1.03E-06
vg0427421479 sf0427236343 4 27421479 1.53E-06 1.53E-06
vg1221167547 sf1221134093 12 21167547 1.72E-06 1.72E-06
vg0620733763 sf0620732766 6 20733763 2.32E-06 2.31E-06
vg0620775608 sf0620774611 6 20775608 2.47E-06 2.47E-06
vg0140395650 sf0140394607 1 40395650 2.56E-06 2.57E-06
vg0907680610 sf0907679610 9 7680610 2.93E-06 2.94E-06
vg0220342715 sf0220336847 2 20342715 4.18E-06 4.19E-06
vg0716717405 sf0716716412 7 16717405 4.63E-06 4.64E-06