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 mr1108 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 5.19E-48 1.86E-33
vg0610566343 sf0610565344 6 10566343 8.17E-46 1.70E-35
vg0610410785 sf0610409786 6 10410785 7.66E-31 1.07E-17
vg0610755079 sf0610754080 6 10755079 2.84E-30 1.32E-16
vg0610674308 sf0610673309 6 10674308 1.84E-26 5.35E-22
vg0610556004 sf0610555005 6 10556004 1.39E-22 2.93E-16
vg0610626135 sf0610625136 6 10626135 1.09E-18 4.93E-13
vg0617319066 sf0617318069 6 17319066 8.76E-18 7.21E-06
vg0610872827 sf0610871828 6 10872827 1.45E-17 1.21E-06
vg0610609111 sf0610608112 6 10609111 3.19E-17 4.91E-11
vg0610674740 sf0610673741 6 10674740 4.58E-17 5.18E-13
vg0611561542 sf0611560543 6 11561542 1.95E-16 4.79E-12
vg0610435285 sf0610434286 6 10435285 3.08E-15 1.13E-14
vg0610875498 sf0610874499 6 10875498 7.46E-15 1.27E-08
vg0610679932 sf0610678933 6 10679932 1.31E-14 1.92E-17
vg0611493106 sf0611492107 6 11493106 2.01E-14 3.99E-09
vg0611466166 sf0611465167 6 11466166 1.38E-13 1.88E-09
vg0609677935 sf0609676936 6 9677935 1.79E-13 1.08E-08
vg1009646441 sf1009575262 10 9646441 7.84E-13 2.57E-07
vg0617595576 sf0617594579 6 17595576 2.30E-11 1.58E-07
vg0612092828 sf0612091829 6 12092828 2.78E-11 2.48E-08
vg0611098317 sf0611097318 6 11098317 1.77E-10 4.47E-09
vg0610127588 sf0610126589 6 10127588 NA 7.86E-12
vg0611646456 sf0611645457 6 11646456 NA 9.48E-10
vg0610205289 sf0610204290 6 10205289 NA 1.55E-07
vg0618988041 sf0618987044 6 18988041 NA 3.38E-07
vg0515926609 sf0515869116 5 15926609 NA 4.83E-07
vg0223043170 sf0223037301 2 23043170 NA 4.19E-06