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 mr1022 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
vg1215977007 sf1215974303 12 15977007 8.93E-103 5.38E-48
vg1209571445 sf1209568854 12 9571445 8.35E-66 2.67E-23
vg1210693559 sf1210690972 12 10693559 1.83E-61 1.70E-24
vg1223872806 sf1223839259 12 23872806 6.52E-49 7.31E-10
vg1223872832 sf1223839285 12 23872832 9.37E-45 2.74E-10
vg1212726422 sf1212723761 12 12726422 9.16E-34 6.92E-09
vg0410423427 sf0410414126 4 10423427 2.20E-29 1.12E-08
vg1219911712 sf1219883182 12 19911712 5.64E-27 4.93E-08
vg1017708903 sf1017637676 10 17708903 9.59E-24 2.99E-07
vg0318960151 sf0318958911 3 18960151 8.79E-19 4.97E-08
vg1215653764 sf1215651061 12 15653764 2.11E-18 3.91E-11
vg0408411178 sf0408406452 4 8411178 3.48E-15 2.62E-07
vg1214849387 sf1214846728 12 14849387 4.59E-15 3.11E-12
vg1214706284 sf1214703625 12 14706284 3.06E-13 3.54E-07
vg1216280437 sf1216277733 12 16280437 NA 8.89E-12
vg1207816760 sf1207814166 12 7816760 NA 4.00E-09
vg1215976836 sf1215974132 12 15976836 NA 5.82E-09
vg1215306532 sf1215303830 12 15306532 NA 5.04E-08
vg0402345102 sf0402340697 4 2345102 NA 1.20E-07
vg1214834250 sf1214831591 12 14834250 NA 1.57E-07
vg0922029772 sf0922029291 9 22029772 NA 3.05E-07
vg1216291337 sf1216288633 12 16291337 NA 4.74E-07
vg1223678969 sf1223645422 12 23678969 NA 5.64E-07