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 mr1270 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
vg0709162379 sf0709161385 7 9162379 7.86E-08 7.86E-08
vg0406861879 sf0406857324 4 6861879 8.37E-08 8.37E-08
vg0406862378 sf0406857823 4 6862378 1.32E-07 1.32E-07
vg0709588264 sf0709587270 7 9588264 3.69E-07 3.69E-07
vg1017098057 sf1017026829 10 17098057 9.26E-07 9.26E-07
vg0235126648 sf0235120779 2 35126648 1.82E-06 1.82E-06
vg0711409773 sf0711408779 7 11409773 1.90E-06 1.90E-06
vg0729692653 sf0729691661 7 29692653 2.56E-06 2.56E-06
vg0113806881 sf0113805855 1 13806881 3.12E-06 3.12E-06
vg0705087105 sf0705086106 7 5087105 3.55E-06 3.55E-06
vg1020009101 sf1019937600 10 20009101 3.96E-06 3.96E-06