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 mr1651 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
vg0414319578 sf0414310291 4 14319578 2.55E-07 2.55E-07
vg0701188850 sf0701187850 7 1188850 5.35E-07 5.35E-07
vg0142427760 sf0142426716 1 42427760 7.21E-07 7.17E-07
vg0421220373 sf0421048425 4 21220373 2.19E-06 2.20E-06
vg0420718113 sf0420546156 4 20718113 2.29E-06 2.30E-06
vg0607562910 sf0607561911 6 7562910 2.50E-06 2.51E-06
vg1208774399 sf1208771806 12 8774399 3.12E-06 3.13E-06
vg1209949245 sf1209946655 12 9949245 4.22E-06 4.23E-06
vg0626149778 sf0626148781 6 26149778 8.08E-06 8.05E-06