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 mr1682 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
vg1219072596 sf1219044032 12 19072596 4.67E-07 4.67E-07
vg1219071207 sf1219042643 12 19071207 5.20E-07 5.20E-07
vg1213932089 sf1213929427 12 13932089 5.89E-07 5.89E-07
vg1217645915 sf1217639870 12 17645915 6.22E-07 6.22E-07
vg1219727877 sf1219699347 12 19727877 1.60E-06 1.60E-06
vg1215998159 sf1215995455 12 15998159 1.91E-06 1.91E-06
vg1218885143 sf1218856578 12 18885143 2.37E-06 2.37E-06
vg1218043542 sf1218014978 12 18043542 4.24E-06 4.25E-06
vg1125722116 sf1125255955 11 25722116 4.28E-06 4.28E-06
vg0502049793 sf0502049775 5 2049793 4.66E-06 4.66E-06