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 mr1954 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
vg0433705748 sf0433520630 4 33705748 8.29E-08 8.29E-08
vg0209814096 sf0209814094 2 9814096 1.73E-07 1.73E-07
vg0135058442 sf0135057399 1 35058442 2.75E-07 2.75E-07
vg0805485086 sf0805484089 8 5485086 5.02E-07 5.02E-07
vg0220727676 sf0220721808 2 20727676 1.88E-06 1.88E-06
vg1106199277 sf1106195029 11 6199277 2.87E-06 2.87E-06
vg0135054438 sf0135053395 1 35054438 2.97E-06 2.97E-06
vg0906350119 sf0906349119 9 6350119 4.32E-06 4.32E-06