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 mr1023 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 2.63E-50 2.50E-25
vg1215968758 sf1215966054 12 15968758 6.19E-49 7.71E-26
vg1210693559 sf1210690972 12 10693559 9.92E-38 2.38E-16
vg1210649746 sf1210647159 12 10649746 2.65E-36 3.04E-17
vg1223872806 sf1223839259 12 23872806 1.38E-29 6.20E-08
vg1213439429 sf1213436767 12 13439429 2.25E-21 4.88E-07
vg1219911712 sf1219883182 12 19911712 9.28E-20 NA
vg1215653080 sf1215650377 12 15653080 2.25E-14 2.34E-08
vg1216422627 sf1216419920 12 16422627 2.33E-13 6.88E-07
vg1215646445 sf1215643742 12 15646445 3.41E-13 1.98E-07
vg1004210744 sf1004127464 10 4210744 3.89E-13 7.10E-07
vg0217672570 sf0217666700 2 17672570 4.50E-13 1.20E-06
vg1214706284 sf1214703625 12 14706284 5.22E-13 2.58E-07
vg0512660263 sf0512603185 5 12660263 8.26E-13 3.40E-07
vg0509824052 sf0509823981 5 9824052 7.57E-12 3.01E-07
vg1207811491 sf1207808897 12 7811491 2.93E-10 2.19E-08
vg1216729879 sf1216723833 12 16729879 3.55E-10 1.82E-07
vg1214847524 sf1214844865 12 14847524 1.72E-09 1.91E-07
vg1216279961 sf1216277257 12 16279961 NA 1.55E-09
vg0416574457 sf0416402498 4 16574457 NA 2.73E-09
vg1205262287 sf1205261273 12 5262287 NA 9.91E-07
vg1214294794 sf1214292134 12 14294794 NA 1.65E-06
vg1215976836 sf1215974132 12 15976836 NA 2.28E-06