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 mr1489 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
vg1215968758 sf1215966054 12 15968758 3.87E-39 6.11E-24
vg1209233335 sf1209230744 12 9233335 1.47E-30 6.25E-16
vg1210649746 sf1210647159 12 10649746 1.68E-30 2.43E-18
vg1223872806 sf1223839259 12 23872806 2.60E-22 1.60E-07
vg1223914996 sf1223881449 12 23914996 6.55E-20 5.41E-08
vg1212938220 sf1212935559 12 12938220 4.00E-19 2.38E-08
vg1213246999 sf1213244337 12 13246999 3.83E-17 4.91E-08
vg1210598082 sf1210595495 12 10598082 7.29E-15 2.49E-08
vg1214706284 sf1214703625 12 14706284 3.10E-14 3.77E-09
vg1215886165 sf1215883461 12 15886165 8.87E-14 1.46E-08
vg0419507153 sf0419335191 4 19507153 1.06E-13 3.92E-07
vg0217672570 sf0217666700 2 17672570 1.64E-13 1.81E-09
vg1207811491 sf1207808897 12 7811491 8.83E-13 8.52E-11
vg1217530188 sf1217524143 12 17530188 3.35E-12 1.63E-07
vg1215646445 sf1215643742 12 15646445 6.77E-11 1.39E-08
vg0405089398 sf0405084839 4 5089398 2.65E-10 4.35E-08
vg0416574457 sf0416402498 4 16574457 2.73E-10 2.98E-10
vg1205718847 sf1205716942 12 5718847 1.37E-09 4.92E-07
vg1216747487 sf1216741441 12 16747487 1.79E-09 4.30E-07
vg1214513714 sf1214511055 12 14513714 9.81E-09 2.86E-07
vg1217326666 sf1217320621 12 17326666 1.56E-08 5.75E-08
vg1216279961 sf1216277257 12 16279961 3.49E-08 1.07E-09
vg0412916634 sf0412907342 4 12916634 NA 7.89E-07
vg1122183927 sf1121717798 11 22183927 NA 9.72E-06