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 mr1083 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
vg0719140447 sf0719139454 7 19140447 3.27E-46 4.70E-27
vg0719049906 sf0719048913 7 19049906 9.59E-45 4.71E-36
vg0707772632 sf0707771637 7 7772632 1.67E-37 NA
vg0704641028 sf0704640029 7 4641028 1.16E-36 NA
vg0626853373 sf0626852376 6 26853373 2.46E-36 3.39E-08
vg0305665264 sf0305664264 3 5665264 3.02E-36 NA
vg0626879116 sf0626878119 6 26879116 1.31E-35 6.85E-10
vg0719091461 sf0719090468 7 19091461 NA 6.29E-27
vg0719145578 sf0719144585 7 19145578 NA 8.68E-25
vg0719156649 sf0719155656 7 19156649 NA 1.52E-23
vg0719105731 sf0719104738 7 19105731 NA 5.41E-23
vg0719065396 sf0719064403 7 19065396 NA 3.87E-21
vg0707667722 sf0707666727 7 7667722 NA 4.32E-16
vg0719154140 sf0719153147 7 19154140 NA 1.94E-15
vg0719466615 sf0719465622 7 19466615 NA 2.37E-15
vg0828401472 sf0828398758 8 28401472 NA 1.96E-14
vg0719452729 sf0719451736 7 19452729 NA 5.73E-14
vg0719436399 sf0719435406 7 19436399 NA 7.99E-14
vg0113087370 sf0113086344 1 13087370 NA 4.53E-13
vg0719047961 sf0719046968 7 19047961 NA 4.88E-11
vg0408294758 sf0408290032 4 8294758 NA 1.33E-10
vg1217507757 sf1217501712 12 17507757 NA 1.34E-10
vg0704482336 sf0704481337 7 4482336 NA 1.83E-10
vg0616953325 sf0616952328 6 16953325 NA 2.25E-10
vg0309319838 sf0309318774 3 9319838 NA 2.77E-10
vg0302581223 sf0302580219 3 2581223 NA 4.87E-10
vg0709019375 sf0709018381 7 9019375 NA 6.94E-10
vg0608463867 sf0608462868 6 8463867 NA 1.10E-09
vg0719618102 sf0719617109 7 19618102 NA 1.29E-09
vg0718996417 sf0718995424 7 18996417 NA 6.16E-07