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 mr1178 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
vg1215977007 sf1215974303 12 15977007 1.67E-100 1.05E-44
vg1209571445 sf1209568854 12 9571445 1.11E-71 2.66E-27
vg1223872806 sf1223839259 12 23872806 9.95E-46 3.41E-07
vg1212726422 sf1212723761 12 12726422 4.38E-31 4.61E-08
vg0410423427 sf0410414126 4 10423427 1.40E-29 3.10E-09
vg1219911712 sf1219883182 12 19911712 4.13E-27 8.55E-08
vg1017708903 sf1017637676 10 17708903 3.57E-24 2.67E-09
vg1214872776 sf1214870117 12 14872776 1.83E-20 1.45E-08
vg0217462869 sf0217456999 2 17462869 5.66E-20 6.93E-08
vg0707316720 sf0707315725 7 7316720 2.21E-17 4.74E-07
vg0404659256 sf0404654695 4 4659256 1.09E-15 5.57E-07
vg1214839103 sf1214836444 12 14839103 2.26E-15 3.75E-12
vg1215063155 sf1215060497 12 15063155 4.29E-15 1.72E-06
vg1216279538 sf1216276834 12 16279538 NA 3.88E-11
vg1215976836 sf1215974132 12 15976836 NA 6.09E-08
vg0405058837 sf0405054276 4 5058837 NA 8.91E-08
vg0224176408 sf0224170539 2 24176408 NA 1.10E-07
vg0406166109 sf0406161549 4 6166109 NA 1.23E-07
vg1216192002 sf1216189298 12 16192002 NA 2.71E-07
vg1210641830 sf1210639243 12 10641830 NA 8.71E-07