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 mr1070 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
vg0719049906 sf0719048913 7 19049906 7.38E-68 1.27E-32
vg0305665264 sf0305664264 3 5665264 1.33E-53 NA
vg0917918788 sf0917917787 9 17918788 3.22E-52 NA
vg0504619344 sf0504619321 5 4619344 3.77E-52 NA
vg0706838922 sf0706837927 7 6838922 2.12E-51 NA
vg0706752672 sf0706751677 7 6752672 2.06E-48 2.39E-06
vg0428520912 sf0428335765 4 28520912 1.10E-47 NA
vg0626897338 sf0626896341 6 26897338 5.66E-47 7.46E-07
vg0719091461 sf0719090468 7 19091461 NA 4.01E-24
vg0719055344 sf0719054351 7 19055344 NA 5.25E-20
vg0719188413 sf0719187420 7 19188413 NA 1.52E-13
vg0719067465 sf0719066472 7 19067465 NA 1.53E-10
vg0718985745 sf0718984752 7 18985745 NA 2.95E-10
vg0719466615 sf0719465622 7 19466615 NA 4.84E-09
vg0315307278 sf0315305925 3 15307278 NA 2.18E-08
vg1002954217 sf1002953194 10 2954217 NA 6.23E-08
vg0113087370 sf0113086344 1 13087370 NA 9.21E-08
vg0828401472 sf0828398758 8 28401472 NA 1.12E-07
vg0302581223 sf0302580219 3 2581223 NA 1.29E-07
vg0719618102 sf0719617109 7 19618102 NA 1.61E-07
vg0900936968 sf0900935968 9 936968 NA 2.70E-07
vg0616962436 sf0616961439 6 16962436 NA 2.97E-07
vg0719153233 sf0719152240 7 19153233 NA 3.76E-07
vg0230189175 sf0230183306 2 30189175 NA 1.32E-06
vg0408294186 sf0408289460 4 8294186 NA 1.65E-06
vg0707667722 sf0707666727 7 7667722 NA 1.78E-06
vg0601621892 sf0601620893 6 1621892 NA 2.03E-06
vg1103514429 sf1103510332 11 3514429 NA 2.24E-06
vg0719452729 sf0719451736 7 19452729 NA 2.82E-06
vg0316256342 sf0316254990 3 16256342 NA 4.37E-06