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 mr1155 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
vg0719047931 sf0719046938 7 19047931 1.14E-56 3.82E-35
vg0719208938 sf0719207945 7 19208938 2.08E-41 5.86E-18
vg0719065253 sf0719064260 7 19065253 1.24E-28 4.30E-32
vg0715953641 sf0715952648 7 15953641 5.94E-28 3.75E-07
vg0715949888 sf0715948895 7 15949888 8.19E-28 2.76E-07
vg0703330513 sf0703329514 7 3330513 1.68E-27 NA
vg0719454357 sf0719453364 7 19454357 2.15E-27 6.70E-07
vg0718964255 sf0718963262 7 18964255 1.38E-21 5.58E-09
vg0617227477 sf0617226480 6 17227477 2.20E-21 NA
vg0315353447 sf0315352094 3 15353447 2.74E-21 2.23E-06
vg0719197671 sf0719196678 7 19197671 NA 5.48E-17
vg0719436399 sf0719435406 7 19436399 NA 3.23E-11
vg0719040981 sf0719039988 7 19040981 NA 1.67E-10
vg0719403111 sf0719402118 7 19403111 NA 1.17E-09
vg0719271354 sf0719270361 7 19271354 NA 6.23E-08
vg1217081938 sf1217075893 12 17081938 NA 1.19E-07
vg1207863655 sf1207861061 12 7863655 NA 2.69E-07
vg0719408893 sf0719407900 7 19408893 NA 3.98E-07
vg0901040131 sf0901039131 9 1040131 NA 9.15E-07
vg0910413877 sf0910412876 9 10413877 NA 1.10E-06
vg0906916912 sf0906915912 9 6916912 NA 3.94E-06
vg0122438890 sf0122437845 1 22438890 NA 4.55E-06