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 mr1926 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
vg1122897896 sf1122431767 11 22897896 1.59E-08 1.59E-08
vg1119409410 sf1118943098 11 19409410 4.96E-08 4.96E-08
vg0900273978 sf0900272978 9 273978 5.54E-08 5.54E-08
vg0209236687 sf0209236685 2 9236687 6.71E-08 6.71E-08
vg0410386441 sf0410377140 4 10386441 9.23E-08 9.23E-08
vg0204707409 sf0204707406 2 4707409 1.77E-07 1.77E-07
vg0332475546 sf0332468419 3 32475546 2.10E-07 2.10E-07
vg0806551012 sf0806550017 8 6551012 2.28E-07 2.28E-07
vg0127823831 sf0127822787 1 27823831 3.08E-07 3.08E-07
vg1222758888 sf1222725327 12 22758888 6.58E-07 6.58E-07
vg0601604412 sf0601603413 6 1604412 6.84E-07 6.84E-07
vg0209349449 sf0209349447 2 9349449 6.96E-07 6.96E-07
vg0321300282 sf0321298792 3 21300282 7.98E-07 7.98E-07
vg1214626036 sf1214623376 12 14626036 8.92E-07 8.92E-07
vg1210160121 sf1210157532 12 10160121 1.49E-06 1.49E-06
vg0140209581 sf0140208538 1 40209581 1.62E-06 1.62E-06
vg0601102379 sf0601101380 6 1102379 1.71E-06 1.71E-06
vg0711712757 sf0711711763 7 11712757 2.06E-06 2.06E-06
vg1214660699 sf1214658039 12 14660699 2.21E-06 2.21E-06
vg0119570175 sf0119569130 1 19570175 2.37E-06 2.37E-06
vg0314422629 sf0314421318 3 14422629 2.40E-06 2.40E-06
vg1214618945 sf1214616285 12 14618945 4.97E-06 4.97E-06