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 mr1188 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
vg0235365192 sf0235359323 2 35365192 1.92E-14 2.55E-11
vg1108673107 sf1108667717 11 8673107 5.35E-14 8.54E-09
vg1108626672 sf1108621282 11 8626672 3.00E-13 3.21E-11
vg0203671161 sf0203671158 2 3671161 6.78E-11 4.00E-06
vg0320735515 sf0320734025 3 20735515 3.38E-10 NA
vg0622020773 sf0622019776 6 22020773 4.98E-10 3.22E-07
vg1124217261 sf1123751131 11 24217261 6.82E-10 1.27E-06
vg0125025708 sf0125024664 1 25025708 1.62E-09 5.45E-07
vg1121302509 sf1120836387 11 21302509 2.87E-09 3.30E-06
vg0523609640 sf0523547061 5 23609640 4.35E-09 2.43E-06
vg0125134011 sf0125132967 1 25134011 5.30E-09 2.74E-07
vg1100538307 sf1100537310 11 538307 5.64E-09 7.54E-08
vg1006722269 sf1006737892 10 6722269 1.37E-08 8.90E-07
vg1214837584 sf1214834925 12 14837584 6.17E-08 9.16E-07
vg0630786990 sf0630785992 6 30786990 9.39E-08 5.19E-07
vg0206427310 sf0206427310 2 6427310 1.01E-07 8.74E-09
vg0319057447 sf0319056207 3 19057447 1.10E-07 5.27E-07
vg0113475773 sf0113474747 1 13475773 1.34E-07 4.36E-07
vg0235259229 sf0235253360 2 35259229 1.74E-07 1.85E-07
vg0203032931 sf0203032929 2 3032931 3.77E-07 2.99E-07
vg0523543573 sf0523480994 5 23543573 1.31E-06 1.31E-06
vg1114018010 sf1113554331 11 14018010 NA 1.04E-07
vg0804452573 sf0804451576 8 4452573 NA 1.60E-07
vg0433807001 sf0433621889 4 33807001 NA 9.44E-07
vg1114010891 sf1113547212 11 14010891 NA 2.02E-06