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 mr1490 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
vg1215977007 sf1215974303 12 15977007 6.20E-81 2.95E-37
vg1209571445 sf1209568854 12 9571445 9.95E-56 1.75E-21
vg1223872806 sf1223839259 12 23872806 7.36E-44 3.81E-09
vg1223827289 sf1223793742 12 23827289 1.02E-39 2.69E-09
vg1212726422 sf1212723761 12 12726422 8.90E-29 1.51E-08
vg0410423427 sf0410414126 4 10423427 3.77E-25 1.74E-07
vg1214872776 sf1214870117 12 14872776 3.16E-18 1.49E-07
vg1215629389 sf1215626686 12 15629389 6.38E-18 1.42E-09
vg1215885768 sf1215883064 12 15885768 7.31E-14 3.43E-08
vg1215976836 sf1215974132 12 15976836 1.11E-13 5.25E-10
vg1216278953 sf1216276249 12 16278953 1.49E-13 2.03E-08
vg1214853500 sf1214850841 12 14853500 9.06E-13 1.05E-09
vg1214706284 sf1214703625 12 14706284 3.16E-12 1.04E-07
vg1207570300 sf1207567705 12 7570300 1.07E-11 1.32E-09
vg1216279961 sf1216277257 12 16279961 NA 1.64E-12
vg1217327067 sf1217321022 12 17327067 NA 2.05E-08
vg1223678969 sf1223645422 12 23678969 NA 1.51E-07
vg1207785706 sf1207783112 12 7785706 NA 2.48E-07
vg0224207855 sf0224201986 2 24207855 NA 6.72E-07
vg1216192440 sf1216189736 12 16192440 NA 1.09E-06
vg0401152271 sf0401147821 4 1152271 NA 1.21E-06