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 mr1078 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
vg0610472973 sf0610471974 6 10472973 8.70E-140 2.44E-52
vg0127353137 sf0127352093 1 27353137 4.71E-72 NA
vg0232960344 sf0232954475 2 32960344 1.84E-71 NA
vg0627249569 sf0627248572 6 27249569 1.27E-70 NA
vg0708454760 sf0708453765 7 8454760 2.06E-70 NA
vg0317507945 sf0317506727 3 17507945 3.01E-65 6.12E-07
vg0610532672 sf0610531673 6 10532672 NA 3.21E-18
vg0610763769 sf0610762770 6 10763769 NA 3.88E-14
vg0610444069 sf0610443070 6 10444069 NA 1.68E-10
vg0610029931 sf0610028932 6 10029931 NA 2.52E-10
vg0610134394 sf0610133395 6 10134394 NA 4.59E-09
vg0611127784 sf0611126785 6 11127784 NA 1.37E-08
vg0610014317 sf0610013318 6 10014317 NA 2.56E-08
vg0610495392 sf0610494393 6 10495392 NA 5.33E-08
vg0613809145 sf0613808146 6 13809145 NA 5.58E-08
vg0610446203 sf0610445204 6 10446203 NA 9.74E-08
vg0610587732 sf0610586733 6 10587732 NA 1.50E-07
vg0610472191 sf0610471192 6 10472191 NA 2.50E-07
vg0920308003 sf0920307522 9 20308003 NA 3.91E-07
vg0610723836 sf0610722837 6 10723836 NA 4.12E-07
vg0610685711 sf0610684712 6 10685711 NA 5.37E-07
vg0610393322 sf0610392323 6 10393322 NA 5.93E-07
vg0615334572 sf0615333573 6 15334572 NA 6.65E-07
vg0206102860 sf0206102860 2 6102860 NA 6.89E-07
vg0421466152 sf0421294203 4 21466152 NA 8.70E-07
vg1116393407 sf1115928284 11 16393407 NA 1.87E-06