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 mr1349 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
vg0529499648 sf0529437003 5 29499648 1.12E-09 4.38E-06
vg0619806827 sf0619805830 6 19806827 1.30E-09 7.48E-06
vg0306451367 sf0306450367 3 6451367 3.00E-09 NA
vg0626092352 sf0626091355 6 26092352 9.77E-09 NA
vg0715245766 sf0715244773 7 15245766 1.17E-08 NA
vg1002941211 sf1002940188 10 2941211 1.55E-08 3.45E-07
vg0512292313 sf0512292243 5 12292313 7.97E-08 1.80E-07
vg0922156723 sf0922156242 9 22156723 1.65E-07 1.06E-06
vg1002940641 sf1002939618 10 2940641 1.08E-06 4.81E-06
vg0413407415 sf0413398128 4 13407415 4.29E-06 NA
vg0907512890 sf0907511890 9 7512890 5.00E-06 NA
vg0131564294 sf0131563250 1 31564294 6.07E-06 3.17E-06
vg0527430964 sf0527368320 5 27430964 9.22E-06 NA
vg0707500779 sf0707499784 7 7500779 NA 7.12E-07
vg0721128197 sf0721127204 7 21128197 NA 3.84E-06
vg0711712797 sf0711711803 7 11712797 NA 3.95E-06