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 mr1145 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
vg0719064221 sf0719063228 7 19064221 9.86E-56 2.36E-23
vg0626853373 sf0626852376 6 26853373 5.22E-49 1.00E-06
vg0706847379 sf0706846384 7 6847379 8.55E-49 NA
vg0917918788 sf0917917787 9 17918788 9.53E-48 NA
vg0626833038 sf0626832041 6 26833038 1.05E-47 1.40E-07
vg0305665264 sf0305664264 3 5665264 3.64E-47 NA
vg0719091461 sf0719090468 7 19091461 NA 1.51E-17
vg0719156649 sf0719155656 7 19156649 NA 1.85E-15
vg0719145578 sf0719144585 7 19145578 NA 5.23E-13
vg0719065396 sf0719064403 7 19065396 NA 5.47E-13
vg0828401472 sf0828398758 8 28401472 NA 4.56E-09
vg0707667722 sf0707666727 7 7667722 NA 2.07E-08
vg0719618102 sf0719617109 7 19618102 NA 3.87E-08
vg0709019375 sf0709018381 7 9019375 NA 6.78E-08
vg0719452729 sf0719451736 7 19452729 NA 7.29E-08
vg0718985959 sf0718984966 7 18985959 NA 1.95E-07
vg0616962436 sf0616961439 6 16962436 NA 2.00E-07
vg0408294758 sf0408290032 4 8294758 NA 2.97E-07
vg0302581223 sf0302580219 3 2581223 NA 2.98E-07
vg0719466615 sf0719465622 7 19466615 NA 3.62E-07
vg0419832144 sf0419660181 4 19832144 NA 4.31E-07
vg0113087370 sf0113086344 1 13087370 NA 5.00E-07
vg0309319838 sf0309318774 3 9319838 NA 7.49E-07
vg0909789099 sf0909788098 9 9789099 NA 7.62E-07
vg0821929731 sf0821927018 8 21929731 NA 7.78E-07
vg0127955944 sf0127954900 1 27955944 NA 8.97E-07
vg0704858080 sf0704857081 7 4858080 NA 1.10E-06
vg1217235620 sf1217229575 12 17235620 NA 1.19E-06
vg0821930075 sf0821927362 8 21930075 NA 4.07E-06
vg0115899007 sf0115897981 1 15899007 NA 8.26E-06