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 mr1132 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 1.59E-77 1.21E-34
vg1215968758 sf1215966054 12 15968758 8.15E-77 1.76E-36
vg1209571445 sf1209568854 12 9571445 1.44E-53 1.55E-19
vg1210649746 sf1210647159 12 10649746 5.96E-48 1.69E-20
vg1223872806 sf1223839259 12 23872806 5.22E-40 3.09E-07
vg1223872832 sf1223839285 12 23872832 2.09E-36 1.59E-07
vg1212726422 sf1212723761 12 12726422 4.16E-27 2.03E-08
vg0410423427 sf0410414126 4 10423427 1.38E-22 NA
vg1215886165 sf1215883461 12 15886165 6.48E-19 1.83E-09
vg0217672570 sf0217666700 2 17672570 3.90E-18 5.85E-11
vg1213296734 sf1213294072 12 13296734 4.54E-18 3.64E-07
vg1216593403 sf1216590696 12 16593403 2.21E-16 1.44E-08
vg1214706284 sf1214703625 12 14706284 3.67E-15 5.18E-09
vg1215789548 sf1215786845 12 15789548 1.69E-13 6.07E-07
vg1214847524 sf1214844865 12 14847524 6.74E-13 1.01E-08
vg1215520105 sf1215517402 12 15520105 1.59E-11 1.87E-09
vg1216279961 sf1216277257 12 16279961 NA 3.97E-12
vg1217330392 sf1217324347 12 17330392 NA 2.74E-08
vg1207785706 sf1207783112 12 7785706 NA 3.64E-08
vg0224207855 sf0224201986 2 24207855 NA 5.51E-08
vg0416574457 sf0416402498 4 16574457 NA 3.72E-07
vg1215815980 sf1215813277 12 15815980 NA 6.88E-07
vg0401152271 sf0401147821 4 1152271 NA 7.53E-07
vg1216530604 sf1216527897 12 16530604 NA 8.86E-07
vg1214513714 sf1214511055 12 14513714 NA 1.21E-06