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 mr1855 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
vg0217067757 sf0217061887 2 17067757 3.21E-208 9.52E-91
vg0217102431 sf0217096561 2 17102431 3.56E-203 1.57E-92
vg0217102196 sf0217096326 2 17102196 2.50E-199 1.13E-96
vg0217108842 sf0217102972 2 17108842 2.61E-185 9.80E-68
vg1015182556 sf1015111324 10 15182556 1.11E-66 2.35E-11
vg1220336324 sf1220307766 12 20336324 9.37E-61 1.86E-10
vg0723337151 sf0723336158 7 23337151 2.30E-53 9.81E-08
vg1226816492 sf1226782891 12 26816492 1.01E-51 1.76E-09
vg1108225523 sf1108220133 11 8225523 7.00E-47 8.68E-08
vg1128516527 sf1127993306 11 28516527 8.59E-45 3.99E-17
vg0217370560 sf0217364690 2 17370560 1.67E-34 2.02E-22
vg0216754099 sf0216748229 2 16754099 1.72E-30 1.82E-11
vg1005364284 sf1005380821 10 5364284 1.03E-29 5.88E-09
vg1216728961 sf1216722915 12 16728961 2.80E-28 5.04E-08
vg0217937456 sf0217931587 2 17937456 8.55E-28 7.41E-16
vg0217344818 sf0217338948 2 17344818 8.75E-28 1.30E-18
vg0217126027 sf0217120157 2 17126027 9.38E-26 1.67E-51
vg0216239744 sf0216233874 2 16239744 1.26E-22 6.54E-11
vg0217345118 sf0217339248 2 17345118 NA 6.58E-14
vg0214537778 sf0214531908 2 14537778 NA 3.08E-11
vg0217861925 sf0217856056 2 17861925 NA 1.15E-10
vg0212899554 sf0212899550 2 12899554 NA 7.33E-10
vg0524068712 sf0524006132 5 24068712 NA 2.87E-09