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 mr1150 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
vg0222729090 sf0222723221 2 22729090 1.16E-67 1.03E-31
vg0222725902 sf0222720033 2 22725902 2.20E-32 7.69E-12
vg0602854650 sf0602853651 6 2854650 1.67E-28 NA
vg0906971590 sf0906970590 9 6971590 6.64E-28 NA
vg1223571779 sf1223538239 12 23571779 1.70E-27 NA
vg0700638475 sf0700637475 7 638475 3.51E-27 NA
vg0525210558 sf0525147979 5 25210558 1.18E-24 1.60E-06
vg0917434598 sf0917433597 9 17434598 2.60E-24 4.38E-06
vg0222889740 sf0222883871 2 22889740 7.34E-24 4.21E-10
vg0505887711 sf0505887649 5 5887711 7.51E-24 3.80E-06
vg0315974803 sf0315973450 3 15974803 7.84E-23 3.16E-06
vg0528462620 sf0528399975 5 28462620 1.14E-22 1.43E-07
vg1202288230 sf1202287231 12 2288230 2.12E-22 NA
vg0232342588 sf0232336719 2 32342588 4.70E-22 8.23E-08
vg0219041076 sf0219035208 2 19041076 8.31E-22 2.14E-06
vg0220963033 sf0220957165 2 20963033 1.69E-21 8.12E-06
vg0222573327 sf0222567458 2 22573327 NA 2.69E-14
vg0115320554 sf0115319528 1 15320554 NA 4.64E-07
vg0222828580 sf0222822711 2 22828580 NA 8.92E-07
vg0222729853 sf0222723984 2 22729853 NA 9.87E-07
vg0224872829 sf0224866960 2 24872829 NA 1.06E-06
vg0224246969 sf0224241100 2 24246969 NA 1.23E-06
vg0203269607 sf0203269605 2 3269607 NA 1.29E-06
vg0321955285 sf0321953792 3 21955285 NA 2.44E-06
vg0222634177 sf0222628308 2 22634177 NA 2.53E-06
vg0223508508 sf0223502639 2 23508508 NA 3.00E-06
vg0709350055 sf0709349061 7 9350055 NA 4.15E-06
vg0521957091 sf0521894533 5 21957091 NA 4.89E-06