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 mr1528 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
vg0716362688 sf0716361695 7 16362688 5.50E-11 2.35E-10
vg0717843035 sf0717842042 7 17843035 8.13E-11 7.28E-09
vg1102153284 sf1102149142 11 2153284 7.62E-10 NA
vg0234966943 sf0234961074 2 34966943 2.42E-09 1.27E-06
vg0234957845 sf0234951976 2 34957845 3.36E-09 9.08E-07
vg0717056384 sf0717055391 7 17056384 3.76E-09 5.92E-07
vg0805949886 sf0805948889 8 5949886 5.57E-09 1.05E-07
vg0908682567 sf0908681566 9 8682567 8.78E-09 2.71E-07
vg1117585468 sf1117119325 11 17585468 8.82E-09 1.62E-06
vg0717056890 sf0717055897 7 17056890 1.34E-08 5.76E-07
vg0717124098 sf0717123105 7 17124098 1.60E-08 1.83E-08
vg0715416146 sf0715415153 7 15416146 3.01E-08 3.67E-06
vg0721652148 sf0721651155 7 21652148 3.40E-08 3.26E-06
vg0716089949 sf0716088956 7 16089949 7.39E-08 1.31E-06
vg0717004704 sf0717003711 7 17004704 3.99E-07 5.23E-07
vg0717007313 sf0717006320 7 17007313 4.68E-07 4.39E-06
vg0727501372 sf0727500378 7 27501372 8.10E-07 3.95E-06
vg1123674215 sf1123208085 11 23674215 1.03E-06 4.10E-07
vg0432144497 sf0431959388 4 32144497 1.09E-06 1.79E-06
vg1123990140 sf1123524010 11 23990140 4.75E-06 2.33E-06
vg0716242647 sf0716241654 7 16242647 6.36E-06 1.88E-06
vg0123690615 sf0123689571 1 23690615 6.43E-06 NA