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 mr1586 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
vg0325696417 sf0325694435 3 25696417 3.26E-42 4.79E-36
vg1121970827 sf1121504698 11 21970827 1.01E-14 7.99E-09
vg0400345487 sf0400344487 4 345487 1.12E-13 3.29E-08
vg0222035625 sf0222029756 2 22035625 1.41E-13 4.85E-08
vg1207091088 sf1207089978 12 7091088 1.45E-13 7.34E-09
vg1006070015 sf1006086553 10 6070015 8.14E-13 1.09E-08
vg0327423375 sf0327416428 3 27423375 1.56E-12 1.07E-10
vg1002034525 sf1002033502 10 2034525 2.39E-12 1.30E-08
vg0229389860 sf0229383991 2 29389860 4.77E-12 9.47E-08
vg1012888857 sf1012817672 10 12888857 1.46E-11 3.49E-11
vg0400439184 sf0400438182 4 439184 1.65E-11 1.51E-08
vg0627993076 sf0627992078 6 27993076 2.03E-11 6.95E-08
vg0318271847 sf0318270629 3 18271847 2.14E-11 3.08E-09
vg0416712669 sf0416540713 4 16712669 2.76E-11 6.92E-09
vg0202731072 sf0202731070 2 2731072 3.88E-11 2.30E-08
vg0304791741 sf0304790743 3 4791741 8.11E-11 7.42E-09
vg0322820996 sf0322819485 3 22820996 3.75E-10 4.06E-09
vg1015794218 sf1015722988 10 15794218 5.19E-10 1.94E-08
vg1022397720 sf1022326194 10 22397720 2.03E-09 4.37E-08
vg0225789722 sf0225783853 2 25789722 1.13E-08 5.11E-08
vg0711956562 sf0711955568 7 11956562 3.03E-08 6.52E-08