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 mr1705 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
vg0716444877 sf0716443884 7 16444877 3.25E-15 1.37E-09
vg0423902918 sf0423717777 4 23902918 1.72E-10 NA
vg0714511673 sf0714510680 7 14511673 6.99E-10 NA
vg1108517495 sf1108512105 11 8517495 8.87E-10 7.34E-06
vg0716335933 sf0716334940 7 16335933 9.33E-10 NA
vg1108085174 sf1108080919 11 8085174 1.09E-09 1.24E-06
vg0724526928 sf0724525934 7 24526928 4.75E-09 8.04E-08
vg0724518237 sf0724517243 7 24518237 6.53E-09 1.89E-06
vg0104831719 sf0104830719 1 4831719 1.61E-07 3.93E-06
vg0720451131 sf0720450138 7 20451131 3.24E-07 8.33E-06
vg0818919268 sf0818916555 8 18919268 5.70E-06 NA
vg0706755497 sf0706754502 7 6755497 NA 1.72E-07
vg0233248704 sf0233242835 2 33248704 NA 3.22E-07
vg0500775033 sf0500775015 5 775033 NA 4.27E-07
vg0414057794 sf0414048509 4 14057794 NA 4.91E-07
vg0112196285 sf0112195259 1 12196285 NA 1.46E-06
vg1005529461 sf1005545998 10 5529461 NA 1.61E-06
vg0716365835 sf0716364842 7 16365835 NA 2.32E-06
vg0701222286 sf0701221286 7 1222286 NA 2.47E-06
vg0724401667 sf0724400673 7 24401667 NA 4.95E-06