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 mr1062 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
vg0405650134 sf0405645574 4 5650134 1.64E-20 5.10E-15
vg0408820718 sf0408815994 4 8820718 2.49E-13 5.69E-10
vg0619746470 sf0619745473 6 19746470 1.19E-11 5.99E-06
vg0802994561 sf0802993564 8 2994561 3.02E-11 2.79E-07
vg0301033890 sf0301032888 3 1033890 3.64E-11 3.95E-06
vg0301468632 sf0301467630 3 1468632 6.13E-10 1.58E-06
vg1104365050 sf1104360952 11 4365050 6.35E-10 2.01E-06
vg1119272401 sf1118806089 11 19272401 6.89E-10 2.56E-06
vg0232791648 sf0232785779 2 32791648 8.95E-10 1.63E-06
vg0416026557 sf0415854590 4 16026557 1.12E-09 1.71E-06
vg0727897229 sf0727896236 7 27897229 2.71E-09 2.86E-06
vg0711901487 sf0711900493 7 11901487 4.21E-09 4.02E-06
vg1113597253 sf1113133575 11 13597253 7.24E-09 1.33E-06
vg0412754396 sf0412745106 4 12754396 1.13E-08 8.77E-07
vg0405268315 sf0405263756 4 5268315 3.67E-08 4.46E-06
vg0714250056 sf0714249063 7 14250056 7.38E-08 NA
vg0620496522 sf0620495525 6 20496522 9.43E-08 9.48E-07
vg0405740436 sf0405735875 4 5740436 3.43E-07 1.81E-08
vg0500210918 sf0500210918 5 210918 NA 4.39E-06
vg0225847151 sf0225841282 2 25847151 NA 4.50E-06