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 mr1261 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
vg1009667343 sf1009596164 10 9667343 5.89E-12 1.38E-07
vg1006507018 sf1006522641 10 6507018 2.85E-11 3.47E-07
vg1201300655 sf1201299655 12 1300655 5.73E-11 2.26E-08
vg1201244694 sf1201243694 12 1244694 1.26E-10 1.03E-08
vg1006345850 sf1006361473 10 6345850 1.65E-10 1.67E-07
vg1010015339 sf1009944160 10 10015339 5.69E-10 3.26E-07
vg1010661385 sf1010590206 10 10661385 8.57E-10 2.54E-07
vg1005523151 sf1005539688 10 5523151 1.01E-09 5.16E-07
vg0716541730 sf0716540737 7 16541730 1.02E-07 3.84E-07
vg0917477265 sf0917476264 9 17477265 1.56E-07 4.28E-06
vg0527609874 sf0527547231 5 27609874 3.10E-07 1.84E-06
vg0501245720 sf0501245704 5 1245720 4.12E-07 1.36E-06
vg1207276357 sf1207273764 12 7276357 6.76E-07 1.80E-06
vg0622495472 sf0622494475 6 22495472 2.60E-06 3.10E-06
vg0115927658 sf0115926632 1 15927658 NA 1.45E-06
vg1111511705 sf1111506022 11 11511705 NA 1.88E-06