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 mr1735 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
vg1217993198 sf1217964634 12 17993198 6.68E-09 4.03E-06
vg0130372159 sf0130371115 1 30372159 7.64E-09 NA
vg1207053263 sf1207052153 12 7053263 9.16E-09 NA
vg0724004854 sf0724003860 7 24004854 1.42E-08 1.22E-06
vg1221796124 sf1221762671 12 21796124 2.13E-08 NA
vg1208634025 sf1208631432 12 8634025 4.60E-08 1.48E-06
vg0217476457 sf0217470587 2 17476457 1.56E-06 NA
vg0800596392 sf0800595392 8 596392 1.62E-06 3.71E-06
vg0128438602 sf0128437557 1 28438602 3.18E-06 NA
vg0217637634 sf0217631764 2 17637634 7.02E-06 2.42E-06
vg1125281578 sf1124815418 11 25281578 NA 1.80E-06
vg1017942904 sf1017871676 10 17942904 NA 1.92E-06
vg0317321849 sf0317320659 3 17321849 NA 2.86E-06
vg0127316647 sf0127315603 1 27316647 NA 3.25E-06
vg0605513869 sf0605512870 6 5513869 NA 4.33E-06
vg1125279042 sf1124812882 11 25279042 NA 4.80E-06
vg0917117261 sf0917116260 9 17117261 NA 8.67E-06