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 mr1123 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
vg0222679274 sf0222673405 2 22679274 6.55E-55 1.45E-22
vg0222693356 sf0222687487 2 22693356 2.31E-54 5.03E-24
vg1110107976 sf1110102553 11 10107976 1.25E-35 3.42E-08
vg0702563509 sf0702562510 7 2563509 1.18E-34 2.16E-07
vg0624499979 sf0624498982 6 24499979 3.39E-34 5.77E-11
vg0818212763 sf0818210050 8 18212763 1.22E-33 2.59E-09
vg1110425815 sf1110420360 11 10425815 8.19E-33 2.24E-08
vg1204557439 sf1204556427 12 4557439 9.81E-33 4.26E-10
vg0314739384 sf0314738071 3 14739384 2.67E-31 1.85E-08
vg0528516881 sf0528454236 5 28516881 1.59E-28 2.12E-07
vg0825885835 sf0825883121 8 25885835 2.17E-28 1.29E-07
vg0316147114 sf0316145761 3 16147114 3.12E-28 5.92E-09
vg0335906768 sf0335899637 3 35906768 6.24E-28 1.65E-08
vg0434845674 sf0434660565 4 34845674 6.66E-27 2.05E-09
vg0222722554 sf0222716685 2 22722554 NA 3.70E-12
vg0802090518 sf0802089521 8 2090518 NA 1.52E-09
vg0141558120 sf0141557077 1 41558120 NA 6.04E-09
vg0222709250 sf0222703381 2 22709250 NA 6.91E-09
vg0327037726 sf0327030779 3 27037726 NA 9.65E-09
vg0141556686 sf0141555643 1 41556686 NA 1.67E-08
vg0222952563 sf0222946694 2 22952563 NA 1.82E-08
vg0822417948 sf0822415235 8 22417948 NA 5.97E-08
vg0819594931 sf0819592218 8 19594931 NA 6.52E-08
vg0420998565 sf0420826617 4 20998565 NA 8.30E-08
vg1200551682 sf1200550682 12 551682 NA 1.44E-07
vg1218455068 sf1218426504 12 18455068 NA 1.94E-07
vg0222714048 sf0222708179 2 22714048 NA 3.22E-07
vg0804649551 sf0804648554 8 4649551 NA 9.90E-06