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 mr1144 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
vg0610567538 sf0610566539 6 10567538 2.17E-115 6.45E-40
vg0610608095 sf0610607096 6 10608095 1.05E-111 9.50E-41
vg0304920678 sf0304919680 3 4920678 7.51E-64 NA
vg0233932146 sf0233926277 2 33932146 1.82E-63 NA
vg0428554389 sf0428369241 4 28554389 2.00E-60 NA
vg0423897544 sf0423712402 4 23897544 4.95E-60 NA
vg0610532672 sf0610531673 6 10532672 NA 1.79E-19
vg0610752378 sf0610751379 6 10752378 NA 7.79E-16
vg0610444069 sf0610443070 6 10444069 NA 3.48E-15
vg0610763769 sf0610762770 6 10763769 NA 2.63E-14
vg0610444061 sf0610443062 6 10444061 NA 4.42E-13
vg0610134394 sf0610133395 6 10134394 NA 2.36E-11
vg0609929059 sf0609928060 6 9929059 NA 3.19E-09
vg0610281727 sf0610280728 6 10281727 NA 5.59E-09
vg0610685711 sf0610684712 6 10685711 NA 1.11E-08
vg0617630534 sf0617629537 6 17630534 NA 3.89E-07
vg0610082555 sf0610081556 6 10082555 NA 5.89E-07
vg0610630630 sf0610629631 6 10630630 NA 6.33E-07
vg0403215241 sf0403210844 4 3215241 NA 7.26E-07
vg0611127784 sf0611126785 6 11127784 NA 7.40E-07
vg0619171840 sf0619170843 6 19171840 NA 7.49E-07
vg0610478852 sf0610477853 6 10478852 NA 8.47E-07
vg0615907055 sf0615906057 6 15907055 NA 8.71E-07
vg0612257913 sf0612256914 6 12257913 NA 9.00E-07
vg0524300922 sf0524238341 5 24300922 NA 1.58E-06
vg0610495466 sf0610494467 6 10495466 NA 2.04E-06
vg0610089141 sf0610088142 6 10089141 NA 2.07E-06
vg0920307704 sf0920307223 9 20307704 NA 2.53E-06
vg0520272922 sf0520210395 5 20272922 NA 3.38E-06
vg0524368371 sf0524305792 5 24368371 NA 5.07E-06