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 mr1193 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
vg0327579645 sf0327572698 3 27579645 4.12E-27 1.10E-11
vg0327580307 sf0327573360 3 27580307 6.59E-27 8.38E-13
vg0130564948 sf0130563904 1 30564948 2.18E-17 NA
vg0134573656 sf0134572613 1 34573656 1.84E-16 NA
vg0113518004 sf0113516978 1 13518004 2.27E-15 NA
vg0907053460 sf0907052460 9 7053460 8.58E-15 NA
vg0525838153 sf0525775574 5 25838153 1.41E-12 4.51E-06
vg1017944597 sf1017873369 10 17944597 2.63E-12 2.23E-06
vg0327557116 sf0327550169 3 27557116 7.75E-12 4.43E-09
vg0327478719 sf0327471772 3 27478719 NA 1.33E-11
vg0327770292 sf0327763345 3 27770292 NA 1.59E-07
vg0327810553 sf0327803607 3 27810553 NA 2.10E-07
vg0806300284 sf0806299289 8 6300284 NA 3.84E-07
vg1121620131 sf1121154008 11 21620131 NA 1.34E-06
vg0402649721 sf0402645325 4 2649721 NA 1.53E-06
vg0142374984 sf0142373940 1 42374984 NA 1.55E-06
vg0142380984 sf0142379940 1 42380984 NA 1.55E-06
vg0142373253 sf0142372209 1 42373253 NA 2.82E-06
vg1119485070 sf1119018758 11 19485070 NA 3.25E-06
vg0315259700 sf0315258347 3 15259700 NA 3.55E-06
vg0301368204 sf0301367202 3 1368204 NA 3.85E-06
vg1215630177 sf1215627474 12 15630177 NA 5.27E-06