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 mr1792 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
vg1014024679 sf1013953445 10 14024679 6.81E-09 8.19E-07
vg1014019486 sf1013948252 10 14019486 7.48E-09 4.99E-07
vg0503455480 sf0503455457 5 3455480 9.81E-09 4.44E-08
vg1214643661 sf1214641001 12 14643661 8.11E-08 NA
vg1009637244 sf1009566065 10 9637244 2.01E-07 NA
vg1218024972 sf1217996408 12 18024972 2.56E-07 4.15E-06
vg1014025113 sf1013953879 10 14025113 6.35E-07 1.32E-06
vg0619955116 sf0619954119 6 19955116 6.71E-06 3.29E-06
vg1209212048 sf1209209457 12 9212048 NA 4.52E-07
vg1214702209 sf1214699550 12 14702209 NA 1.03E-06