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 mr1138 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
vg0916922179 sf0916921178 9 16922179 4.88E-20 1.47E-07
vg0724352464 sf0724351470 7 24352464 8.56E-19 1.61E-06
vg0724527960 sf0724526966 7 24527960 2.14E-17 3.56E-11
vg0611577935 sf0611576936 6 11577935 4.41E-17 NA
vg0215991693 sf0215985823 2 15991693 4.80E-17 NA
vg0618965393 sf0618964396 6 18965393 2.09E-16 NA
vg0217819719 sf0217813850 2 17819719 1.27E-12 5.60E-07
vg0215881021 sf0215875151 2 15881021 3.37E-12 5.27E-07
vg0218064697 sf0218058828 2 18064697 1.10E-11 9.66E-08
vg0611943788 sf0611942789 6 11943788 7.44E-11 NA
vg0916795852 sf0916794851 9 16795852 NA 2.72E-11
vg0724505923 sf0724504929 7 24505923 NA 7.26E-11
vg0800596392 sf0800595392 8 596392 NA 2.22E-10
vg0800104556 sf0800103556 8 104556 NA 4.81E-08
vg0331292058 sf0331284943 3 31292058 NA 6.27E-07
vg1108671668 sf1108666278 11 8671668 NA 7.60E-07
vg0311608269 sf0311606987 3 11608269 NA 8.86E-07
vg1009597003 sf1009525824 10 9597003 NA 9.43E-07
vg0800651704 sf0800650704 8 651704 NA 1.16E-06
vg0331292031 sf0331284916 3 31292031 NA 1.55E-06
vg0918584653 sf0918583652 9 18584653 NA 2.44E-06
vg0431405060 sf0431219958 4 31405060 NA 2.77E-06