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 mr1745 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
vg0430606062 sf0430420937 4 30606062 9.38E-70 7.20E-54
vg0430559445 sf0430374320 4 30559445 1.89E-69 1.79E-58
vg0430645227 sf0430460102 4 30645227 6.72E-53 1.46E-19
vg0430641254 sf0430456129 4 30641254 1.45E-52 4.41E-19
vg0921373579 sf0921373098 9 21373579 5.79E-49 NA
vg0128937112 sf0128936067 1 28937112 2.76E-48 NA
vg0605507888 sf0605506889 6 5507888 9.26E-47 NA
vg0430479634 sf0430294512 4 30479634 NA 7.33E-26
vg0430617232 sf0430432107 4 30617232 NA 3.83E-22
vg0430855895 sf0430670775 4 30855895 NA 2.84E-20
vg0430538279 sf0430353154 4 30538279 NA 1.28E-11
vg0307590023 sf0307588961 3 7590023 NA 1.31E-11
vg0225876283 sf0225870414 2 25876283 NA 2.46E-10
vg0430611308 sf0430426183 4 30611308 NA 2.71E-10
vg0919877661 sf0919877180 9 19877661 NA 4.86E-10
vg0430452456 sf0430267333 4 30452456 NA 6.50E-10
vg0325946462 sf0325944478 3 25946462 NA 1.96E-09
vg0124633522 sf0124632478 1 24633522 NA 2.04E-09
vg0221812870 sf0221807001 2 21812870 NA 3.34E-09
vg1125263510 sf1124797350 11 25263510 NA 3.75E-09
vg0307650234 sf0307649172 3 7650234 NA 1.10E-08
vg1125419173 sf1124953012 11 25419173 NA 1.55E-08
vg0216537545 sf0216531675 2 16537545 NA 1.91E-08
vg0430293825 sf0430108697 4 30293825 NA 2.11E-08
vg0617762306 sf0617761309 6 17762306 NA 2.33E-08
vg0519461555 sf0519399039 5 19461555 NA 2.79E-08
vg0802567454 sf0802566457 8 2567454 NA 3.53E-08
vg0325243401 sf0325241482 3 25243401 NA 4.37E-08
vg0701099543 sf0701098543 7 1099543 NA 4.39E-08
vg1015968448 sf1015897219 10 15968448 NA 9.85E-08
vg1121984717 sf1121518588 11 21984717 NA 1.15E-07
vg1122064371 sf1121598242 11 22064371 NA 3.03E-07
vg1100882780 sf1100881781 11 882780 NA 3.99E-07