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 mr1367 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
vg0620514412 sf0620513415 6 20514412 9.14E-08 9.14E-08
vg0620514657 sf0620513660 6 20514657 2.33E-07 2.33E-07
vg0102330722 sf0102329722 1 2330722 3.01E-07 3.01E-07
vg0921518541 sf0921518060 9 21518541 7.35E-07 7.35E-07
vg1023002650 sf1022931123 10 23002650 1.05E-06 1.05E-06
vg1109322931 sf1109317508 11 9322931 2.85E-06 2.85E-06
vg1125905500 sf1125439419 11 25905500 4.60E-06 4.61E-06