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 mr1390 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 3.94E-98 2.94E-45
vg1209571445 sf1209568854 12 9571445 2.53E-65 4.19E-25
vg1210450037 sf1210447450 12 10450037 2.01E-59 4.06E-25
vg1223872806 sf1223839259 12 23872806 5.55E-50 3.59E-09
vg1223827289 sf1223793742 12 23827289 5.63E-45 6.47E-10
vg1212726422 sf1212723761 12 12726422 6.13E-32 4.95E-09
vg0410423427 sf0410414126 4 10423427 6.36E-27 4.38E-07
vg1219373193 sf1219344662 12 19373193 1.85E-26 1.53E-07
vg1214874442 sf1214871783 12 14874442 3.20E-19 7.18E-10
vg1215610968 sf1215608265 12 15610968 2.80E-16 9.22E-08
vg1215646445 sf1215643742 12 15646445 3.63E-16 2.49E-09
vg1214839103 sf1214836444 12 14839103 2.16E-15 1.33E-11
vg1214706284 sf1214703625 12 14706284 9.28E-14 5.85E-09
vg1215885768 sf1215883064 12 15885768 1.50E-13 3.01E-08
vg1216278953 sf1216276249 12 16278953 2.09E-13 4.77E-08
vg1216279961 sf1216277257 12 16279961 NA 3.72E-12
vg1207816955 sf1207814361 12 7816955 NA 1.02E-09
vg1223678969 sf1223645422 12 23678969 NA 2.94E-09
vg0224207855 sf0224201986 2 24207855 NA 3.56E-08
vg1217330392 sf1217324347 12 17330392 NA 8.40E-08
vg0416574457 sf0416402498 4 16574457 NA 3.32E-07
vg1215976836 sf1215974132 12 15976836 NA 3.66E-07
vg0401152271 sf0401147821 4 1152271 NA 4.87E-07