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 mr1754 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
vg0501809181 sf0501809164 5 1809181 8.50E-11 1.10E-07
vg0607991416 sf0607990417 6 7991416 3.00E-10 8.12E-09
vg1100909838 sf1100908839 11 909838 9.18E-10 7.54E-06
vg0601870760 sf0601869761 6 1870760 2.50E-09 NA
vg0527284387 sf0527221743 5 27284387 2.55E-09 NA
vg0504496077 sf0504496054 5 4496077 4.77E-09 2.87E-06
vg0907175535 sf0907174535 9 7175535 5.60E-09 7.10E-07
vg0232755756 sf0232749887 2 32755756 9.56E-09 1.23E-08
vg0906814901 sf0906813901 9 6814901 4.48E-08 2.74E-06
vg0616750117 sf0616749119 6 16750117 4.67E-08 4.55E-06
vg0910121829 sf0910120828 9 10121829 2.35E-07 NA
vg1216527792 sf1216525085 12 16527792 2.45E-07 NA
vg0706562208 sf0706561213 7 6562208 3.97E-07 NA
vg0500831115 sf0500831097 5 831115 4.41E-07 2.28E-06
vg0407736903 sf0407732170 4 7736903 NA 5.18E-07
vg0608003490 sf0608002491 6 8003490 NA 5.76E-07
vg0825824337 sf0825821623 8 25824337 NA 6.05E-07
vg1226730127 sf1226696525 12 26730127 NA 1.57E-06
vg0501780326 sf0501780309 5 1780326 NA 3.80E-06
vg0804933121 sf0804932124 8 4933121 NA 4.59E-06