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 mr1245 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
vg0321477334 sf0321475844 3 21477334 3.98E-12 NA
vg0922565216 sf0922564735 9 22565216 1.15E-10 NA
vg0317011545 sf0317010419 3 17011545 3.54E-10 NA
vg0919489568 sf0919489158 9 19489568 1.12E-09 NA
vg0302287012 sf0302286008 3 2287012 1.16E-09 NA
vg1221632629 sf1221599176 12 21632629 6.26E-07 NA
vg1201206550 sf1201205550 12 1206550 8.32E-07 NA
vg0413095791 sf0413086501 4 13095791 8.72E-07 NA
vg0505632591 sf0505632529 5 5632591 NA 1.33E-06
vg0505864665 sf0505864603 5 5864665 NA 1.39E-06
vg0801474449 sf0801473451 8 1474449 NA 2.55E-06
vg1218884427 sf1218855862 12 18884427 NA 2.86E-06
vg1222786386 sf1222752825 12 22786386 NA 3.59E-06
vg1124343343 sf1123877187 11 24343343 NA 6.59E-06