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 mr1439 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
vg0318756417 sf0318755177 3 18756417 5.24E-13 3.94E-07
vg0318756422 sf0318755182 3 18756422 2.94E-12 1.36E-06
vg0318928238 sf0318926998 3 18928238 4.09E-12 6.06E-10
vg0320911578 sf0320910088 3 20911578 7.98E-12 1.61E-10
vg0320620607 sf0320619117 3 20620607 8.55E-12 2.89E-10
vg1102378940 sf1102374799 11 2378940 2.52E-11 NA
vg1117157515 sf1116691367 11 17157515 3.66E-11 NA
vg0319437084 sf0319435595 3 19437084 8.79E-11 NA
vg0318331646 sf0318330428 3 18331646 1.08E-10 2.76E-09
vg0410291056 sf0410281754 4 10291056 8.04E-10 9.42E-08
vg0403196295 sf0403191898 4 3196295 1.23E-09 1.25E-08
vg0608860704 sf0608859705 6 8860704 2.46E-09 3.66E-07
vg0310177475 sf0310176391 3 10177475 1.19E-08 NA
vg0406883539 sf0406878798 4 6883539 1.40E-08 3.92E-06
vg0721964052 sf0721963059 7 21964052 3.19E-08 NA
vg0121623910 sf0121622865 1 21623910 1.04E-07 NA
vg0319975449 sf0319973960 3 19975449 NA 2.76E-07
vg0820374951 sf0820372238 8 20374951 NA 9.39E-07
vg0420830218 sf0420658261 4 20830218 NA 2.36E-06
vg0720025470 sf0720024477 7 20025470 NA 3.09E-06