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 mr1878 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 1.97E-51 1.18E-15
vg0719182554 sf0719181561 7 19182554 2.09E-50 1.85E-23
vg0719064221 sf0719063228 7 19064221 2.11E-39 2.11E-21
vg0724227387 sf0724226393 7 24227387 2.42E-39 NA
vg0305696088 sf0305695088 3 5696088 2.75E-39 NA
vg0607484677 sf0607483678 6 7484677 8.06E-39 NA
vg0705233181 sf0705232182 7 5233181 1.88E-38 NA
vg0719063095 sf0719062102 7 19063095 4.72E-36 1.46E-11
vg0719091461 sf0719090468 7 19091461 NA 4.48E-17
vg0719156146 sf0719155153 7 19156146 NA 5.07E-13
vg0719432287 sf0719431294 7 19432287 NA 8.19E-10
vg0719466615 sf0719465622 7 19466615 NA 4.05E-09
vg0719346699 sf0719345706 7 19346699 NA 5.49E-08
vg0719507177 sf0719506184 7 19507177 NA 6.43E-08
vg0719304244 sf0719303251 7 19304244 NA 1.20E-07
vg0719065396 sf0719064403 7 19065396 NA 1.44E-07
vg0718959080 sf0718958087 7 18959080 NA 2.16E-07
vg0401160495 sf0401156045 4 1160495 NA 6.37E-07
vg0714249785 sf0714248792 7 14249785 NA 7.32E-07
vg0401150253 sf0401145803 4 1150253 NA 7.70E-07
vg0719144059 sf0719143066 7 19144059 NA 7.81E-07
vg1207833484 sf1207830890 12 7833484 NA 1.07E-06
vg0719128589 sf0719127596 7 19128589 NA 1.60E-06
vg0401152900 sf0401148450 4 1152900 NA 3.76E-06
vg0107208536 sf0107207536 1 7208536 NA 4.55E-06