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 mr1082 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
vg0719067465 sf0719066472 7 19067465 3.90E-18 1.36E-14
vg0719006525 sf0719005532 7 19006525 4.26E-18 1.41E-14
vg0130825775 sf0130824731 1 30825775 6.56E-12 NA
vg0909749678 sf0909748677 9 9749678 2.91E-11 NA
vg0417642687 sf0417470728 4 17642687 3.34E-11 1.78E-06
vg0107198487 sf0107197487 1 7198487 3.47E-11 4.84E-06
vg0130826614 sf0130825570 1 30826614 1.51E-10 2.28E-06
vg0130662242 sf0130661198 1 30662242 1.56E-10 7.58E-06
vg1213429246 sf1213426584 12 13429246 2.33E-10 3.83E-06
vg0136510873 sf0136509830 1 36510873 8.93E-10 1.73E-06
vg1101911438 sf1101910439 11 1911438 1.69E-09 9.49E-08
vg0714249785 sf0714248792 7 14249785 1.94E-07 2.72E-06
vg0811122646 sf0811121651 8 11122646 3.26E-07 1.47E-06
vg0719049421 sf0719048428 7 19049421 1.53E-06 2.91E-14
vg0210890398 sf0210890396 2 10890398 NA 1.55E-06