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 mr1920 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
vg0604160684 sf0604159685 6 4160684 6.33E-37 2.95E-13
vg0604247093 sf0604246094 6 4247093 1.46E-33 4.54E-15
vg0311195243 sf0311193961 3 11195243 7.54E-31 NA
vg0527265673 sf0527203029 5 27265673 1.98E-28 NA
vg0122917286 sf0122916242 1 22917286 2.55E-28 NA
vg0327376146 sf0327369199 3 27376146 5.05E-28 8.25E-07
vg0311698039 sf0311696757 3 11698039 3.35E-27 3.53E-07
vg1001168844 sf1001167820 10 1168844 6.58E-27 6.09E-08
vg0118369451 sf0118368405 1 18369451 6.48E-24 6.84E-07
vg1022854220 sf1022782693 10 22854220 7.47E-24 9.88E-07
vg0326981451 sf0326974504 3 26981451 2.08E-22 1.93E-06
vg0604726687 sf0604725688 6 4726687 NA 1.18E-08
vg0604237628 sf0604236629 6 4237628 NA 1.69E-07
vg0326933756 sf0326926809 3 26933756 NA 6.41E-07
vg1001183960 sf1001182937 10 1183960 NA 1.09E-06
vg1218169236 sf1218140672 12 18169236 NA 1.11E-06
vg1011809445 sf1011738260 10 11809445 NA 1.25E-06
vg0604184640 sf0604183641 6 4184640 NA 2.18E-06
vg0208546299 sf0208546298 2 8546299 NA 2.80E-06
vg0127297735 sf0127296691 1 27297735 NA 2.91E-06
vg0604418262 sf0604417263 6 4418262 NA 3.07E-06