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 mr1117 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
vg1009043049 sf1008971910 10 9043049 5.42E-16 6.25E-11
vg1008520987 sf1008449849 10 8520987 9.59E-16 3.34E-11
vg1006353771 sf1006369394 10 6353771 1.24E-13 5.12E-08
vg1204314449 sf1204313437 12 4314449 4.61E-13 4.28E-09
vg0407822984 sf0407818252 4 7822984 4.98E-12 3.08E-07
vg1006304251 sf1006319874 10 6304251 7.26E-12 2.38E-07
vg1005923799 sf1005940337 10 5923799 6.38E-11 4.24E-07
vg1216843191 sf1216837145 12 16843191 7.18E-11 3.77E-07
vg1223473790 sf1223440250 12 23473790 4.76E-10 7.29E-07
vg0501793703 sf0501793686 5 1793703 2.65E-09 1.08E-07
vg0334662669 sf0334655539 3 34662669 1.15E-08 5.21E-06
vg0916693881 sf0916692880 9 16693881 1.77E-08 3.40E-06
vg0403205910 sf0403201513 4 3205910 2.45E-08 7.55E-07
vg0708524273 sf0708523278 7 8524273 2.62E-08 5.09E-07
vg0334657752 sf0334650622 3 34657752 3.63E-08 2.89E-06
vg0619894434 sf0619893437 6 19894434 6.29E-08 1.96E-06
vg0504390095 sf0504390072 5 4390095 1.17E-07 3.54E-06
vg0335323103 sf0335315972 3 35323103 1.98E-07 1.02E-06
vg0402649523 sf0402645127 4 2649523 1.56E-06 5.51E-07
vg0109359620 sf0109358596 1 9359620 2.52E-06 NA
vg0335767966 sf0335760835 3 35767966 2.63E-06 1.10E-06
vg1113389475 sf1112925796 11 13389475 7.01E-06 8.16E-06
vg0417689977 sf0417518018 4 17689977 NA 3.11E-07
vg0920451675 sf0920451194 9 20451675 NA 1.10E-06
vg1010541730 sf1010470551 10 10541730 NA 1.49E-06
vg0403136466 sf0403132069 4 3136466 NA 2.34E-06