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 mr1865 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
vg0922415213 sf0922414732 9 22415213 2.96E-102 1.21E-23
vg0922416727 sf0922416246 9 22416727 1.07E-93 8.04E-20
vg0922428117 sf0922427636 9 22428117 1.20E-87 3.76E-34
vg0916404897 sf0916403896 9 16404897 1.71E-80 NA
vg0304866487 sf0304865489 3 4866487 6.39E-78 NA
vg0309927258 sf0309926194 3 9927258 2.58E-77 NA
vg1203225321 sf1203224324 12 3225321 3.98E-76 NA
vg0717006246 sf0717005253 7 17006246 2.19E-71 2.66E-06
vg0613084325 sf0613083326 6 13084325 4.20E-69 7.90E-07
vg0922436617 sf0922436136 9 22436617 NA 6.97E-21
vg0922417122 sf0922416641 9 22417122 NA 3.17E-17
vg0922451431 sf0922450950 9 22451431 NA 9.42E-13
vg0922560785 sf0922560304 9 22560785 NA 1.51E-10
vg0922565216 sf0922564735 9 22565216 NA 1.35E-07
vg0922403934 sf0922403453 9 22403934 NA 1.73E-07
vg0922300827 sf0922300346 9 22300827 NA 2.01E-07
vg0904740928 sf0904739928 9 4740928 NA 2.70E-07
vg0922494091 sf0922493610 9 22494091 NA 2.71E-07
vg0912946767 sf0912945766 9 12946767 NA 2.43E-06
vg0330337817 sf0330330856 3 30337817 NA 3.72E-06
vg0922202326 sf0922201845 9 22202326 NA 4.29E-06