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 mr1408 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
vg0719044743 sf0719043750 7 19044743 4.03E-17 8.56E-18
vg0719436399 sf0719435406 7 19436399 3.86E-15 9.82E-13
vg0719452729 sf0719451736 7 19452729 1.22E-14 8.89E-10
vg0707667722 sf0707666727 7 7667722 2.82E-14 1.63E-08
vg0704482336 sf0704481337 7 4482336 5.36E-14 9.49E-08
vg0623040717 sf0623039720 6 23040717 7.06E-14 4.09E-08
vg0627197504 sf0627196507 6 27197504 6.83E-13 1.03E-07
vg0620536797 sf0620535800 6 20536797 1.11E-12 4.92E-08
vg0419905874 sf0419733910 4 19905874 4.22E-12 7.15E-09
vg0309319838 sf0309318774 3 9319838 6.85E-11 1.57E-07
vg0704858080 sf0704857081 7 4858080 7.22E-11 1.22E-08
vg0719063677 sf0719062684 7 19063677 3.84E-10 1.45E-13
vg0616962436 sf0616961439 6 16962436 1.06E-09 1.20E-08
vg0626833038 sf0626832041 6 26833038 1.15E-09 4.97E-09
vg0719052201 sf0719051208 7 19052201 1.07E-08 1.25E-16
vg0228543492 sf0228537623 2 28543492 1.35E-07 NA
vg0719140447 sf0719139454 7 19140447 1.67E-07 3.16E-10
vg0719150486 sf0719149493 7 19150486 NA 4.46E-11
vg0408294758 sf0408290032 4 8294758 NA 4.54E-10
vg0719335714 sf0719334721 7 19335714 NA 1.92E-09
vg0828401472 sf0828398758 8 28401472 NA 2.80E-09
vg0719377504 sf0719376511 7 19377504 NA 4.88E-09
vg0719042144 sf0719041151 7 19042144 NA 5.62E-09
vg0719042209 sf0719041216 7 19042209 NA 5.68E-09
vg1217302382 sf1217296337 12 17302382 NA 1.33E-08
vg0709019375 sf0709018381 7 9019375 NA 5.71E-08
vg0616985717 sf0616984720 6 16985717 NA 7.29E-08