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 mr1173 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
vg0511085884 sf0511085813 5 11085884 1.12E-07 1.12E-07
vg0512797069 sf0512739991 5 12797069 1.50E-07 1.50E-07
vg1125670130 sf1125203969 11 25670130 1.95E-07 1.95E-07
vg1207301608 sf1207299015 12 7301608 2.37E-07 2.37E-07
vg0513751374 sf0513693918 5 13751374 3.15E-07 3.15E-07
vg0508131496 sf0508131436 5 8131496 1.91E-06 1.91E-06
vg1126088739 sf1125617153 11 26088739 3.16E-06 3.16E-06