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 mr1269 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
vg1105906564 sf1105902316 11 5906564 6.47E-09 3.50E-06
vg1217039777 sf1217033731 12 17039777 4.16E-08 NA
vg0501904125 sf0501904107 5 1904125 6.91E-08 7.90E-06
vg1105448751 sf1105444502 11 5448751 7.42E-08 NA
vg1105431576 sf1105427327 11 5431576 7.69E-08 NA
vg0420788121 sf0420616164 4 20788121 5.39E-07 1.46E-06
vg0310177475 sf0310176391 3 10177475 1.23E-06 4.86E-06
vg0421025376 sf0420853429 4 21025376 5.30E-06 NA
vg1216906679 sf1216900633 12 16906679 9.71E-06 NA
vg0520332453 sf0520269926 5 20332453 NA 8.76E-07
vg0420830764 sf0420658807 4 20830764 NA 1.73E-06