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 mr1226 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
vg0719007567 sf0719006574 7 19007567 1.99E-23 5.16E-13
vg0719001862 sf0719000869 7 19001862 3.01E-22 4.27E-15
vg0719140489 sf0719139496 7 19140489 2.48E-21 4.33E-13
vg0719231703 sf0719230710 7 19231703 7.53E-18 1.79E-08
vg1201356688 sf1201355688 12 1356688 4.88E-16 8.84E-10
vg0717197101 sf0717196108 7 17197101 1.52E-15 3.97E-09
vg0315778980 sf0315777627 3 15778980 4.04E-15 1.39E-08
vg0707706006 sf0707705011 7 7706006 2.37E-14 1.05E-07
vg0305260839 sf0305259839 3 5260839 8.72E-14 8.60E-08
vg0504617447 sf0504617424 5 4617447 6.69E-13 5.86E-11
vg1214370012 sf1214367353 12 14370012 1.01E-12 1.32E-07
vg1210300519 sf1210297932 12 10300519 3.44E-12 9.24E-07
vg1201578984 sf1201577984 12 1578984 6.96E-12 1.05E-06
vg0610070340 sf0610069341 6 10070340 1.11E-11 3.80E-07
vg1209292727 sf1209290137 12 9292727 3.09E-11 5.99E-06
vg0429428460 sf0429243327 4 29428460 3.44E-11 1.40E-07
vg0717317743 sf0717316750 7 17317743 4.82E-11 9.97E-08
vg0721118397 sf0721117404 7 21118397 3.50E-08 7.61E-07
vg0620278958 sf0620277961 6 20278958 1.25E-07 5.25E-07
vg0719095798 sf0719094805 7 19095798 2.39E-07 4.29E-06
vg0504291251 sf0504291228 5 4291251 4.00E-07 1.87E-07
vg0719475676 sf0719474683 7 19475676 NA 1.96E-07
vg0405231183 sf0405226624 4 5231183 NA 4.60E-07
vg0226057933 sf0226052064 2 26057933 NA 1.07E-06