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 mr1670 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
vg0138139604 sf0138138561 1 38139604 6.74E-66 1.80E-17
vg0138163036 sf0138161993 1 38163036 1.85E-64 2.72E-16
vg1119431785 sf1118965473 11 19431785 2.93E-53 NA
vg0914952639 sf0914951638 9 14952639 5.82E-52 9.09E-06
vg0135577045 sf0135576002 1 35577045 2.30E-51 NA
vg0229905485 sf0229899616 2 29905485 4.29E-50 NA
vg0140952929 sf0140951886 1 40952929 6.18E-50 3.53E-07
vg0323622322 sf0323620496 3 23622322 3.13E-48 4.36E-06
vg0103791160 sf0103790160 1 3791160 4.49E-48 3.74E-06
vg0220807490 sf0220801622 2 20807490 6.46E-48 2.53E-06
vg0400468558 sf0400467556 4 468558 NA 3.67E-22
vg0400436102 sf0400435100 4 436102 NA 4.00E-19
vg0400388457 sf0400387455 4 388457 NA 3.11E-09
vg0400442191 sf0400441189 4 442191 NA 4.19E-09
vg0400033101 sf0400032101 4 33101 NA 5.77E-08
vg0400380170 sf0400379168 4 380170 NA 7.37E-08
vg1221512382 sf1221478929 12 21512382 NA 1.24E-07
vg0400415140 sf0400414138 4 415140 NA 1.96E-07
vg0213970538 sf0213964668 2 13970538 NA 7.87E-07
vg0610435245 sf0610434246 6 10435245 NA 8.23E-07
vg0507535621 sf0507535562 5 7535621 NA 8.42E-07
vg0334773462 sf0334766332 3 34773462 NA 9.28E-07
vg0803472333 sf0803471336 8 3472333 NA 1.29E-06
vg0401225828 sf0401221378 4 1225828 NA 1.63E-06
vg0400006669 sf0400005669 4 6669 NA 2.07E-06
vg1216441109 sf1216438402 12 16441109 NA 2.64E-06
vg0820151458 sf0820148745 8 20151458 NA 2.93E-06
vg0400066292 sf0400065292 4 66292 NA 3.02E-06
vg0213924621 sf0213918751 2 13924621 NA 3.37E-06
vg0400034660 sf0400033660 4 34660 NA 3.53E-06
vg0921524582 sf0921524101 9 21524582 NA 3.72E-06
vg0802917283 sf0802916286 8 2917283 NA 4.08E-06
vg0820145252 sf0820142539 8 20145252 NA 5.75E-06