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 mr1088 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
vg0719007567 sf0719006574 7 19007567 6.34E-33 1.05E-24
vg0719136412 sf0719135419 7 19136412 5.96E-16 9.27E-11
vg1201654412 sf1201653412 12 1654412 1.29E-11 1.98E-06
vg0719274779 sf0719273786 7 19274779 4.03E-11 4.82E-12
vg0718862824 sf0718861831 7 18862824 4.18E-11 7.77E-08
vg0707515285 sf0707514290 7 7515285 6.63E-11 1.41E-06
vg0315179733 sf0315178380 3 15179733 3.42E-10 1.66E-06
vg1202102394 sf1202101392 12 2102394 4.85E-10 7.46E-07
vg0305031973 sf0305030975 3 5031973 6.97E-10 7.30E-07
vg0720408008 sf0720407015 7 20408008 1.19E-09 1.81E-06
vg0719139080 sf0719138087 7 19139080 5.31E-08 3.35E-06
vg0718886158 sf0718885165 7 18886158 1.67E-07 2.18E-06
vg0106693959 sf0106692959 1 6693959 3.99E-07 NA
vg1105944153 sf1105939905 11 5944153 8.12E-07 3.64E-06
vg0718961954 sf0718960961 7 18961954 NA 2.62E-09
vg0719499891 sf0719498898 7 19499891 NA 4.79E-07
vg0503840950 sf0503840927 5 3840950 NA 4.39E-06
vg1124078018 sf1123611888 11 24078018 NA 4.41E-06