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 mr1871 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
vg0226044873 sf0226039004 2 26044873 4.22E-12 2.65E-09
vg0403328670 sf0403324273 4 3328670 1.32E-09 1.15E-07
vg0223207791 sf0223201922 2 23207791 2.23E-09 1.60E-06
vg1208562683 sf1208560090 12 8562683 3.48E-09 1.06E-08
vg0313437671 sf0313436389 3 13437671 4.14E-09 2.38E-06
vg0117840935 sf0117839889 1 17840935 2.60E-08 1.72E-07
vg0200617583 sf0200617583 2 617583 1.57E-07 4.63E-06
vg1204021413 sf1204020401 12 4021413 2.99E-07 8.59E-07
vg1221569648 sf1221536195 12 21569648 1.91E-06 6.50E-07
vg1005997118 sf1006013656 10 5997118 6.70E-06 8.71E-06
vg0113575626 sf0113574600 1 13575626 NA 7.42E-07
vg0113605352 sf0113604326 1 13605352 NA 4.50E-06