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 mr1234 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
vg0610564701 sf0610563702 6 10564701 3.79E-40 3.21E-20
vg0610459095 sf0610458096 6 10459095 9.42E-37 5.97E-23
vg0610360715 sf0610359716 6 10360715 1.43E-23 1.95E-11
vg0610412338 sf0610411339 6 10412338 1.64E-22 1.80E-10
vg0616119655 sf0616118657 6 16119655 3.13E-18 3.71E-06
vg0617319066 sf0617318069 6 17319066 3.26E-18 5.81E-07
vg0612996928 sf0612995929 6 12996928 1.25E-17 5.60E-07
vg0610646456 sf0610645457 6 10646456 4.28E-17 9.53E-10
vg0610683007 sf0610682008 6 10683007 1.12E-16 7.59E-13
vg0609930953 sf0609929954 6 9930953 2.68E-16 7.71E-11
vg0719037241 sf0719036248 7 19037241 1.52E-14 NA
vg0610792367 sf0610791368 6 10792367 1.17E-12 2.34E-07
vg0610872423 sf0610871424 6 10872423 2.94E-12 2.29E-07
vg0614543893 sf0614542894 6 14543893 1.65E-10 3.35E-06
vg0610613426 sf0610612427 6 10613426 8.30E-10 1.58E-06
vg0617807141 sf0617806144 6 17807141 1.38E-09 4.48E-06
vg0610709208 sf0610708209 6 10709208 3.56E-09 7.39E-07
vg0623041409 sf0623040412 6 23041409 1.69E-08 4.77E-06
vg0612586290 sf0612585291 6 12586290 NA 1.82E-07
vg0226057933 sf0226052064 2 26057933 NA 5.68E-07
vg0617636590 sf0617635593 6 17636590 NA 1.43E-06
vg0121366875 sf0121365830 1 21366875 NA 1.61E-06
vg0613018813 sf0613017814 6 13018813 NA 3.36E-06
vg0207433349 sf0207433349 2 7433349 NA 4.48E-06
vg0407665649 sf0407660916 4 7665649 NA 4.78E-06
vg0611125937 sf0611124938 6 11125937 NA 4.87E-06