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 mr1519 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
vg0115147411 sf0115146385 1 15147411 1.77E-24 3.61E-15
vg0115386399 sf0115385373 1 15386399 2.72E-23 3.88E-15
vg0117665352 sf0117664306 1 17665352 1.99E-20 4.70E-12
vg0115284393 sf0115283367 1 15284393 3.94E-18 4.45E-10
vg0320043666 sf0320042177 3 20043666 5.10E-18 1.85E-09
vg0114024172 sf0114023146 1 14024172 8.94E-15 4.35E-07
vg0114152917 sf0114151891 1 14152917 1.03E-14 6.30E-08
vg1205988878 sf1205987859 12 5988878 4.06E-14 7.57E-08
vg0715489455 sf0715488462 7 15489455 7.17E-14 9.72E-07
vg0315264922 sf0315263569 3 15264922 2.84E-12 6.73E-07
vg0334627622 sf0334620492 3 34627622 1.52E-11 2.75E-06
vg1126193023 sf1125721437 11 26193023 2.32E-11 5.98E-07
vg0412900448 sf0412891156 4 12900448 2.87E-11 4.71E-08
vg1215107089 sf1215104426 12 15107089 9.09E-11 1.61E-07
vg1119865923 sf1119399846 11 19865923 1.51E-10 9.93E-08
vg0814797975 sf0814795261 8 14797975 1.51E-09 1.93E-06
vg0114794253 sf0114793227 1 14794253 2.82E-08 1.03E-06
vg1005044043 sf1005060580 10 5044043 8.38E-08 8.47E-07
vg0919648876 sf0919648466 9 19648876 5.12E-07 NA
vg0624655960 sf0624654963 6 24655960 1.02E-06 1.67E-06
vg1103053802 sf1103049706 11 3053802 1.32E-06 NA
vg0207004176 sf0207004176 2 7004176 1.34E-06 2.57E-07
vg0207316810 sf0207316810 2 7316810 4.03E-06 2.97E-06
vg1000994273 sf1000993249 10 994273 7.05E-06 NA
vg0628564882 sf0628563884 6 28564882 NA 3.51E-08
vg0332529482 sf0332522355 3 32529482 NA 2.71E-06