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 mr1925 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
vg0107115494 sf0107114494 1 7115494 1.98E-09 1.98E-09
vg1125118463 sf1124652303 11 25118463 1.57E-08 1.57E-08
vg0428667722 sf0428482573 4 28667722 4.13E-08 4.13E-08
vg0104297093 sf0104296093 1 4297093 1.09E-07 1.09E-07
vg0106765973 sf0106764973 1 6765973 1.73E-07 1.73E-07
vg0609107545 sf0609106546 6 9107545 3.95E-07 3.95E-07
vg1124875808 sf1124409648 11 24875808 4.38E-07 4.38E-07
vg0625255454 sf0625254457 6 25255454 4.59E-07 4.58E-07
vg0812954188 sf0812952013 8 12954188 8.85E-07 8.85E-07
vg0230090438 sf0230084569 2 30090438 1.53E-06 1.52E-06
vg1218179477 sf1218150913 12 18179477 2.45E-06 2.45E-06
vg0729409966 sf0729408974 7 29409966 3.55E-06 3.55E-06
vg1104020767 sf1104016669 11 4020767 3.84E-06 3.84E-06
vg0408107056 sf0408102330 4 8107056 3.96E-06 3.96E-06
vg0402214005 sf0402209600 4 2214005 4.10E-06 4.10E-06
vg0432714610 sf0432529496 4 32714610 4.75E-06 4.75E-06