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 mr1065 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
vg0610566403 sf0610565404 6 10566403 5.43E-111 2.18E-29
vg0610471911 sf0610470912 6 10471911 1.29E-104 1.48E-31
vg0610183020 sf0610182021 6 10183020 4.89E-87 2.78E-25
vg0616950705 sf0616949708 6 16950705 4.76E-70 NA
vg0719196783 sf0719195790 7 19196783 2.78E-67 NA
vg0708839982 sf0708838987 7 8839982 5.45E-64 NA
vg0304920678 sf0304919680 3 4920678 1.47E-62 NA
vg0617223679 sf0617222682 6 17223679 1.74E-57 8.66E-08
vg0610763769 sf0610762770 6 10763769 NA 3.13E-12
vg0611990477 sf0611989478 6 11990477 NA 9.22E-10
vg0610707600 sf0610706601 6 10707600 NA 5.02E-09
vg0610487099 sf0610486100 6 10487099 NA 5.13E-09
vg0610442278 sf0610441279 6 10442278 NA 6.64E-09
vg0610014317 sf0610013318 6 10014317 NA 8.53E-09
vg0609930953 sf0609929954 6 9930953 NA 9.42E-09
vg0611946117 sf0611945118 6 11946117 NA 1.23E-08
vg0610784437 sf0610783438 6 10784437 NA 2.43E-08
vg0611735326 sf0611734327 6 11735326 NA 6.16E-08
vg0614107939 sf0614106940 6 14107939 NA 8.10E-08
vg0629122299 sf0629121301 6 29122299 NA 1.86E-07
vg0610393322 sf0610392323 6 10393322 NA 3.26E-07
vg0610278393 sf0610277394 6 10278393 NA 3.78E-07
vg0610813890 sf0610812891 6 10813890 NA 4.14E-07
vg0713349047 sf0713348054 7 13349047 NA 4.78E-07
vg0611561341 sf0611560342 6 11561341 NA 6.29E-07
vg0614785443 sf0614784444 6 14785443 NA 9.38E-07
vg0611682950 sf0611681951 6 11682950 NA 2.15E-06
vg0528941797 sf0528879152 5 28941797 NA 2.16E-06
vg0711095110 sf0711094116 7 11095110 NA 2.76E-06
vg0311534838 sf0311533556 3 11534838 NA 3.07E-06
vg0224285609 sf0224279740 2 24285609 NA 3.09E-06