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 mr1411 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
vg0719140489 sf0719139496 7 19140489 8.68E-16 3.44E-10
vg0719001862 sf0719000869 7 19001862 1.83E-15 7.43E-11
vg0717197101 sf0717196108 7 17197101 5.64E-15 1.32E-09
vg1217000030 sf1216993984 12 17000030 6.56E-15 9.16E-08
vg0719007567 sf0719006574 7 19007567 2.88E-14 9.82E-08
vg1201356688 sf1201355688 12 1356688 7.07E-14 2.97E-10
vg0315200001 sf0315198648 3 15200001 1.32E-13 1.95E-07
vg1210372103 sf1210369516 12 10372103 6.55E-13 8.42E-07
vg0323471529 sf0323469703 3 23471529 7.24E-13 2.27E-06
vg0719138048 sf0719137055 7 19138048 7.37E-13 1.54E-06
vg0613011415 sf0613010416 6 13011415 8.01E-13 3.33E-08
vg1201614837 sf1201613837 12 1614837 2.40E-12 8.94E-07
vg1214370012 sf1214367353 12 14370012 2.73E-12 2.60E-07
vg0611336250 sf0611335251 6 11336250 1.26E-11 1.42E-06
vg1201578984 sf1201577984 12 1578984 2.50E-11 2.42E-07
vg0719833084 sf0719832091 7 19833084 7.49E-11 1.24E-06
vg0610070340 sf0610069341 6 10070340 1.20E-09 9.96E-07
vg0719449907 sf0719448914 7 19449907 8.19E-09 1.45E-06
vg0805870856 sf0805869859 8 5870856 8.87E-09 1.12E-06
vg0630441488 sf0630440490 6 30441488 1.80E-08 1.41E-06
vg0211826989 sf0211826985 2 11826989 1.22E-07 3.35E-07
vg0504291251 sf0504291228 5 4291251 NA 1.46E-06
vg1207455286 sf1207452692 12 7455286 NA 1.86E-06