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 mr1369 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
vg0139482305 sf0139481262 1 39482305 1.19E-08 1.19E-08
vg0216113702 sf0216107832 2 16113702 1.50E-07 1.50E-07
vg0712942763 sf0712941770 7 12942763 1.77E-07 1.77E-07
vg0627868980 sf0627867982 6 27868980 1.98E-07 1.98E-07
vg1219543928 sf1219515398 12 19543928 1.99E-07 1.99E-07
vg0123862783 sf0123861739 1 23862783 2.00E-07 2.00E-07
vg0710415797 sf0710414803 7 10415797 2.37E-07 2.37E-07
vg0607075796 sf0607074797 6 7075796 2.73E-07 2.73E-07
vg0505839196 sf0505839134 5 5839196 2.75E-07 2.75E-07
vg0401913477 sf0401909073 4 1913477 3.67E-07 3.67E-07
vg1205690365 sf1205689347 12 5690365 4.58E-07 4.58E-07
vg1209158266 sf1209155675 12 9158266 4.98E-07 4.98E-07
vg0705766254 sf0705765255 7 5766254 5.23E-07 5.23E-07
vg0728714849 sf0728713857 7 28714849 5.93E-07 5.93E-07
vg0824850789 sf0824848075 8 24850789 6.50E-07 6.50E-07
vg0809828408 sf0809827412 8 9828408 6.59E-07 6.59E-07
vg0502115981 sf0502115955 5 2115981 6.77E-07 6.77E-07
vg0812783415 sf0812781240 8 12783415 7.63E-07 7.63E-07
vg0235707769 sf0235701900 2 35707769 9.78E-07 9.78E-07
vg0124008913 sf0124007869 1 24008913 1.27E-06 1.27E-06