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 mr1880 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
vg0431614961 sf0431429856 4 31614961 3.45E-13 NA
vg0402401496 sf0402397091 4 2401496 8.64E-13 3.14E-07
vg0902208073 sf0902207073 9 2208073 1.71E-12 1.12E-07
vg0217809250 sf0217803381 2 17809250 3.11E-12 NA
vg0720631792 sf0720630799 7 20631792 5.16E-12 4.87E-06
vg0427391704 sf0427206568 4 27391704 6.54E-12 2.46E-06
vg0431840206 sf0431655100 4 31840206 1.40E-11 2.53E-06
vg0431615949 sf0431430844 4 31615949 2.62E-11 2.35E-06
vg1011333524 sf1011262344 10 11333524 1.07E-10 4.88E-06
vg0720674612 sf0720673619 7 20674612 1.35E-10 4.61E-06
vg0432280842 sf0432095735 4 32280842 2.10E-09 2.97E-07
vg0223518939 sf0223513070 2 23518939 7.40E-08 4.38E-06
vg0904278800 sf0904277800 9 4278800 1.50E-07 1.52E-06
vg0216878747 sf0216872877 2 16878747 2.75E-07 1.37E-07
vg0400483853 sf0400482851 4 483853 5.69E-07 2.48E-06
vg0915815139 sf0915814138 9 15815139 NA 1.01E-06
vg1114596701 sf1114133019 11 14596701 NA 3.57E-06