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 mr1038 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
vg0729105428 sf0729104436 7 29105428 2.60E-105 2.41E-88
vg1222460913 sf1222427352 12 22460913 1.60E-34 7.56E-24
vg1219585537 sf1219557007 12 19585537 1.91E-27 1.17E-15
vg1107793749 sf1107789494 11 7793749 6.91E-23 7.76E-09
vg0631155509 sf0631154511 6 31155509 1.98E-22 8.30E-10
vg1201520069 sf1201519069 12 1520069 4.31E-22 1.50E-10
vg0333009355 sf0333002225 3 33009355 1.51E-21 6.31E-10
vg0417556620 sf0417384662 4 17556620 1.74E-21 4.74E-15
vg0219834070 sf0219828202 2 19834070 2.63E-21 1.81E-12
vg0108515482 sf0108514482 1 8515482 4.77E-21 2.78E-11
vg0316797922 sf0316796796 3 16797922 3.08E-20 1.22E-10
vg1221198057 sf1221164603 12 21198057 1.46E-19 2.53E-14
vg0726950185 sf0726949191 7 26950185 1.71E-19 4.47E-13
vg1016323870 sf1016252646 10 16323870 2.65E-19 1.33E-13
vg0303857837 sf0303856833 3 3857837 2.68E-19 1.12E-09
vg0226136784 sf0226130915 2 26136784 1.77E-17 1.60E-10
vg0325722534 sf0325720552 3 25722534 2.18E-17 1.12E-09
vg0906859250 sf0906858250 9 6859250 2.49E-17 3.53E-10
vg0522027089 sf0521964531 5 22027089 1.35E-16 5.83E-10
vg0140074301 sf0140073258 1 40074301 8.96E-12 4.70E-10
vg1101299110 sf1101298111 11 1299110 1.81E-11 1.78E-11
vg0401713889 sf0401709438 4 1713889 2.08E-11 4.44E-10