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 mr1959 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
vg1000459276 sf1000458252 10 459276 4.43E-22 5.21E-14
vg1000709547 sf1000708523 10 709547 4.64E-21 3.44E-14
vg1128846586 sf1128323365 11 28846586 2.26E-11 4.47E-07
vg0528039299 sf0527976654 5 28039299 3.26E-11 9.29E-07
vg0330850428 sf0330843315 3 30850428 4.99E-11 1.10E-06
vg0330709449 sf0330702336 3 30709449 6.03E-11 8.13E-07
vg1008206965 sf1008135827 10 8206965 9.29E-11 3.81E-06
vg1124875808 sf1124409648 11 24875808 6.00E-09 2.33E-07
vg1128161380 sf1127638159 11 28161380 4.25E-07 1.06E-06
vg1125103445 sf1124637285 11 25103445 1.46E-06 4.30E-09
vg0224473315 sf0224467446 2 24473315 5.48E-06 8.21E-07
vg1125046291 sf1124580131 11 25046291 NA 3.23E-10
vg1125032015 sf1124565855 11 25032015 NA 4.90E-08
vg1000738566 sf1000737542 10 738566 NA 9.70E-07
vg0301337606 sf0301336604 3 1337606 NA 1.46E-06
vg1125085942 sf1124619782 11 25085942 NA 2.39E-06
vg0528218584 sf0528155939 5 28218584 NA 2.95E-06
vg0907282111 sf0907281111 9 7282111 NA 3.32E-06
vg0431913843 sf0431728738 4 31913843 NA 4.91E-06