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 mr1117 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
vg0222693356 sf0222687487 2 22693356 1.50E-46 1.99E-20
vg0222687210 sf0222681341 2 22687210 1.16E-45 6.56E-21
vg0110304750 sf0110303726 1 10304750 2.87E-29 1.51E-06
vg0505964521 sf0505964460 5 5964521 6.52E-29 7.34E-07
vg1110107976 sf1110102553 11 10107976 7.66E-29 9.89E-08
vg1110591251 sf1110585796 11 10591251 1.42E-28 4.14E-08
vg0505887711 sf0505887649 5 5887711 2.58E-28 1.93E-07
vg1204550069 sf1204549057 12 4550069 3.01E-28 1.35E-08
vg0818212763 sf0818210050 8 18212763 1.64E-27 5.35E-09
vg1204557439 sf1204556427 12 4557439 2.37E-27 1.09E-08
vg0528277698 sf0528215053 5 28277698 7.94E-27 3.47E-08
vg0624499979 sf0624498982 6 24499979 1.45E-26 3.09E-09
vg0500664660 sf0500664660 5 664660 1.58E-26 2.15E-07
vg1117963441 sf1117497299 11 17963441 1.87E-24 2.42E-08
vg0221587673 sf0221581804 2 21587673 1.98E-23 NA
vg0434845674 sf0434660565 4 34845674 8.87E-22 8.54E-08
vg1218456968 sf1218428404 12 18456968 7.91E-20 7.56E-08
vg0222952563 sf0222946694 2 22952563 1.57E-19 5.04E-13
vg0222722554 sf0222716685 2 22722554 NA 7.73E-11
vg0432159315 sf0431974208 4 32159315 NA 7.87E-09
vg1204507349 sf1204506337 12 4507349 NA 1.32E-08
vg0709837237 sf0709836243 7 9837237 NA 3.18E-08
vg0219344371 sf0219338503 2 19344371 NA 4.06E-08
vg0327037726 sf0327030779 3 27037726 NA 4.34E-08
vg1209218924 sf1209216333 12 9218924 NA 5.01E-08
vg0222683259 sf0222677390 2 22683259 NA 1.45E-07
vg0420266563 sf0420094608 4 20266563 NA 1.60E-07
vg1204500338 sf1204499326 12 4500338 NA 1.61E-07
vg0403136311 sf0403131914 4 3136311 NA 1.84E-07
vg0828048682 sf0828045968 8 28048682 NA 2.27E-07
vg0303196975 sf0303195971 3 3196975 NA 2.48E-07
vg0709674359 sf0709673365 7 9674359 NA 6.70E-07
vg0315922266 sf0315920913 3 15922266 NA 2.30E-06