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 mr1131 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
vg0719133785 sf0719132792 7 19133785 1.28E-11 2.79E-10
vg0719090536 sf0719089543 7 19090536 1.62E-11 1.97E-09
vg0719209499 sf0719208506 7 19209499 4.71E-11 8.44E-10
vg0719088533 sf0719087540 7 19088533 5.83E-11 1.89E-09
vg0718885472 sf0718884479 7 18885472 7.81E-09 1.78E-07
vg0519114346 sf0519051830 5 19114346 1.01E-08 NA
vg1101783832 sf1101782833 11 1783832 3.56E-08 NA
vg0304931155 sf0304930157 3 4931155 7.81E-08 3.40E-06
vg1124078478 sf1123612348 11 24078478 3.33E-07 3.43E-07
vg1109949998 sf1109944575 11 9949998 5.70E-06 5.96E-06
vg0908180972 sf0908179972 9 8180972 6.15E-06 NA