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 mr1498 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
vg0106684533 sf0106683533 1 6684533 8.04E-19 8.14E-16
vg0107115494 sf0107114494 1 7115494 3.16E-16 3.99E-14
vg0428667722 sf0428482573 4 28667722 2.06E-12 8.32E-10
vg0418136371 sf0417964414 4 18136371 7.97E-12 1.38E-08
vg0625255454 sf0625254457 6 25255454 9.96E-11 3.59E-08
vg0729409966 sf0729408974 7 29409966 1.23E-10 1.42E-08
vg0432714610 sf0432529496 4 32714610 1.35E-10 1.95E-08
vg0804318898 sf0804317901 8 4318898 1.82E-10 3.18E-07
vg0624011151 sf0624010154 6 24011151 1.92E-10 1.02E-08
vg0906684964 sf0906683964 9 6684964 3.90E-10 1.25E-07
vg0420210561 sf0420038606 4 20210561 8.52E-10 2.46E-08
vg0416189113 sf0416017146 4 16189113 1.69E-09 6.28E-08
vg0505693786 sf0505693724 5 5693786 1.75E-09 3.49E-07
vg0609107545 sf0609106546 6 9107545 2.06E-09 3.00E-08
vg0432735842 sf0432550729 4 32735842 2.26E-09 2.66E-07
vg0310111258 sf0310110194 3 10111258 2.79E-09 2.50E-07
vg0519883737 sf0519821213 5 19883737 2.80E-09 2.45E-07
vg1100973405 sf1100972406 11 973405 4.27E-09 2.34E-07
vg0408107056 sf0408102330 4 8107056 5.63E-09 2.56E-07
vg0104231204 sf0104230204 1 4231204 1.50E-08 2.37E-07
vg1104020767 sf1104016669 11 4020767 2.80E-08 2.16E-07