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 mr1006 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
vg0921454415 sf0921453934 9 21454415 2.25E-22 1.09E-16
vg0921456056 sf0921455575 9 21456056 9.53E-22 5.00E-17
vg0921374162 sf0921373681 9 21374162 3.14E-13 2.68E-09
vg1126773646 sf1126302033 11 26773646 1.26E-09 7.41E-06
vg0808270560 sf0808269564 8 8270560 1.28E-09 NA
vg0922455577 sf0922455096 9 22455577 4.83E-09 NA
vg0504038203 sf0504038180 5 4038203 6.83E-08 7.85E-08
vg0328906605 sf0328899657 3 28906605 2.15E-06 3.44E-06
vg0915096631 sf0915095630 9 15096631 2.15E-06 NA
vg0328872939 sf0328865992 3 28872939 4.02E-06 5.60E-06
vg1204926524 sf1204925509 12 4926524 7.02E-06 NA
vg0913080416 sf0913079415 9 13080416 NA 6.13E-07
vg0921282690 sf0921282209 9 21282690 NA 3.00E-06
vg0614703627 sf0614702628 6 14703627 NA 3.21E-06
vg0205700559 sf0205700559 2 5700559 NA 4.56E-06