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 mr1842 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
vg0404540486 sf0404536089 4 4540486 9.62E-11 1.81E-08
vg0618738950 sf0618737953 6 18738950 5.74E-10 3.85E-09
vg0725325993 sf0725324999 7 25325993 8.44E-10 1.50E-07
vg0103053858 sf0103052858 1 3053858 1.80E-09 4.14E-06
vg0722939064 sf0722938071 7 22939064 2.56E-09 1.09E-07
vg1105316445 sf1105312196 11 5316445 2.56E-08 3.24E-06
vg0621485267 sf0621484270 6 21485267 3.22E-08 3.19E-06
vg0416315085 sf0416143118 4 16315085 3.82E-08 4.58E-07
vg0620831120 sf0620830123 6 20831120 4.30E-08 4.00E-06
vg0414572804 sf0414563518 4 14572804 5.41E-08 4.00E-07
vg1201180694 sf1201179694 12 1180694 7.02E-08 3.86E-06
vg0711326131 sf0711325137 7 11326131 9.80E-08 7.37E-07
vg0725636129 sf0725635135 7 25636129 1.11E-07 5.69E-07
vg0808091194 sf0808090198 8 8091194 2.74E-07 1.49E-07
vg0712740849 sf0712739856 7 12740849 3.10E-07 3.43E-08
vg0714477799 sf0714476806 7 14477799 3.77E-07 1.41E-06
vg0222066693 sf0222060824 2 22066693 4.16E-07 1.08E-06
vg0401023830 sf0401019382 4 1023830 5.32E-07 1.89E-06
vg0619641710 sf0619640713 6 19641710 6.12E-07 2.46E-06
vg0621396998 sf0621396001 6 21396998 4.12E-06 NA
vg0719602226 sf0719601233 7 19602226 9.74E-06 1.33E-07
vg0113570321 sf0113569295 1 13570321 NA 1.07E-06
vg0135107915 sf0135106872 1 35107915 NA 2.75E-06