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 mr1193 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
vg0327579635 sf0327572688 3 27579635 3.57E-21 2.23E-11
vg0326341709 sf0326334757 3 26341709 7.75E-12 NA
vg0113581337 sf0113580311 1 13581337 2.96E-11 NA
vg1221236365 sf1221202911 12 21236365 4.31E-11 NA
vg0329193524 sf0329186576 3 29193524 5.06E-11 NA
vg0327509835 sf0327502888 3 27509835 1.91E-10 1.35E-07
vg0114248557 sf0114247531 1 14248557 4.41E-10 4.52E-06
vg0328874978 sf0328868031 3 28874978 1.10E-09 1.58E-06
vg1223766180 sf1223732633 12 23766180 6.88E-09 NA
vg0114116343 sf0114115317 1 14116343 1.58E-08 NA
vg0142336907 sf0142335863 1 42336907 6.95E-08 NA
vg0114100604 sf0114099578 1 14100604 1.72E-07 8.14E-07
vg0327580144 sf0327573197 3 27580144 3.72E-07 9.97E-10
vg0420830218 sf0420658261 4 20830218 NA 2.11E-06
vg0420823688 sf0420651731 4 20823688 NA 7.80E-06