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 mr1560 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
vg0719001862 sf0719000869 7 19001862 4.66E-43 1.78E-11
vg0719049906 sf0719048913 7 19049906 9.69E-36 4.95E-24
vg0705232840 sf0705231841 7 5232840 1.61E-35 NA
vg0917780861 sf0917779860 9 17780861 2.04E-35 NA
vg0305767833 sf0305766833 3 5767833 2.74E-35 NA
vg0708672267 sf0708671272 7 8672267 3.93E-35 NA
vg0719271739 sf0719270746 7 19271739 NA 9.02E-18
vg0719091461 sf0719090468 7 19091461 NA 5.49E-17
vg0719105731 sf0719104738 7 19105731 NA 7.44E-14
vg0719345198 sf0719344205 7 19345198 NA 5.36E-13
vg0428494128 sf0428308982 4 28494128 NA 4.99E-12
vg0719067465 sf0719066472 7 19067465 NA 4.48E-11
vg0719466615 sf0719465622 7 19466615 NA 1.80E-09
vg0719436399 sf0719435406 7 19436399 NA 5.97E-09
vg0329561125 sf0329554165 3 29561125 NA 6.25E-09
vg0421592157 sf0421420207 4 21592157 NA 1.45E-08
vg0613280290 sf0613279291 6 13280290 NA 1.90E-08
vg1120455169 sf1119989094 11 20455169 NA 2.11E-08
vg0805321651 sf0805320654 8 5321651 NA 2.78E-08
vg1105544417 sf1105540169 11 5544417 NA 3.29E-08
vg0418071652 sf0417899693 4 18071652 NA 4.96E-08
vg0218320728 sf0218314859 2 18320728 NA 5.80E-08
vg1217503545 sf1217497500 12 17503545 NA 8.82E-08
vg0620744993 sf0620743996 6 20744993 NA 9.09E-08
vg0819367990 sf0819365277 8 19367990 NA 9.50E-08
vg0708152905 sf0708151910 7 8152905 NA 1.07E-07
vg0520689110 sf0520626551 5 20689110 NA 1.21E-07
vg0707699197 sf0707698202 7 7699197 NA 1.26E-07
vg0718664463 sf0718663470 7 18664463 NA 2.42E-07
vg0617980791 sf0617979794 6 17980791 NA 2.56E-07
vg1119330153 sf1118863841 11 19330153 NA 2.31E-06