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 mr1409 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
vg0325710457 sf0325708475 3 25710457 2.71E-18 2.71E-18
vg0325696417 sf0325694435 3 25696417 6.76E-18 6.75E-18
vg0222035625 sf0222029756 2 22035625 1.88E-11 1.88E-11
vg0202817095 sf0202817093 2 2817095 2.57E-11 2.57E-11
vg1121714352 sf1121248229 11 21714352 1.01E-10 1.01E-10
vg1127869289 sf1127397675 11 27869289 8.98E-10 8.99E-10
vg0130466262 sf0130465218 1 30466262 5.63E-09 5.63E-09
vg0400345487 sf0400344487 4 345487 1.21E-08 1.21E-08
vg0103658465 sf0103657465 1 3658465 3.03E-08 3.03E-08
vg0631103106 sf0631102108 6 31103106 5.67E-08 5.67E-08
vg0307963417 sf0307962355 3 7963417 7.37E-08 7.37E-08
vg1017929024 sf1017857796 10 17929024 8.29E-08 8.29E-08
vg0423418147 sf0423233002 4 23418147 9.11E-08 9.11E-08
vg1016628078 sf1016556851 10 16628078 9.14E-08 9.14E-08
vg1010153418 sf1010082239 10 10153418 1.02E-07 1.02E-07
vg0228319680 sf0228313811 2 28319680 1.04E-07 1.04E-07
vg1005547004 sf1005563541 10 5547004 1.15E-07 1.15E-07
vg1200840948 sf1200839948 12 840948 1.74E-07 1.74E-07
vg0626022065 sf0626021068 6 26022065 1.82E-07 1.82E-07
vg0318271847 sf0318270629 3 18271847 2.29E-07 2.29E-07
vg0502636698 sf0502636674 5 2636698 4.45E-07 4.45E-07