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 mr1563 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
vg0723340885 sf0723339892 7 23340885 1.67E-38 9.75E-31
vg1219210664 sf1219182134 12 19210664 2.78E-14 1.51E-06
vg1219345800 sf1219317270 12 19345800 1.33E-13 8.60E-07
vg0402918909 sf0402914515 4 2918909 9.37E-13 2.15E-06
vg0400212499 sf0400211499 4 212499 1.60E-12 NA
vg0723501936 sf0723500943 7 23501936 1.63E-11 4.66E-06
vg1101115939 sf1101114940 11 1115939 2.88E-09 1.57E-06
vg1219131671 sf1219103107 12 19131671 4.79E-09 1.10E-06
vg1224247892 sf1224214345 12 24247892 1.50E-08 4.42E-07
vg1010296106 sf1010224927 10 10296106 4.31E-08 1.68E-06
vg1108453091 sf1108447701 11 8453091 1.14E-07 3.87E-06
vg0723547698 sf0723546705 7 23547698 1.29E-07 1.81E-06
vg0807808848 sf0807807852 8 7808848 NA 1.28E-06
vg0525173806 sf0525111227 5 25173806 NA 2.04E-06
vg0427581097 sf0427395958 4 27581097 NA 2.71E-06
vg0221725390 sf0221719521 2 21725390 NA 3.46E-06
vg1225455213 sf1225421608 12 25455213 NA 3.66E-06