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 mr1798 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
vg0402389835 sf0402385430 4 2389835 6.09E-29 6.05E-18
vg0230107152 sf0230101283 2 30107152 6.08E-15 1.45E-06
vg0314426110 sf0314424799 3 14426110 5.66E-13 5.19E-06
vg1122311857 sf1121845728 11 22311857 7.90E-13 4.15E-06
vg0314425542 sf0314424231 3 14425542 1.43E-12 1.56E-06
vg0402466310 sf0402461908 4 2466310 1.39E-11 NA
vg0313160369 sf0313159087 3 13160369 2.65E-11 3.24E-07
vg1010744278 sf1010673099 10 10744278 6.66E-10 1.62E-07
vg0413382497 sf0413373208 4 13382497 4.04E-08 3.91E-06
vg0402032946 sf0402028542 4 2032946 5.34E-08 3.42E-07
vg0400079773 sf0400078773 4 79773 6.66E-08 NA
vg0522576271 sf0522513713 5 22576271 1.56E-07 NA
vg1122195477 sf1121729348 11 22195477 2.53E-07 2.07E-06
vg1017360795 sf1017289568 10 17360795 4.22E-07 2.70E-06
vg0918621961 sf0918620960 9 18621961 6.66E-07 1.03E-06
vg0207309711 sf0207309711 2 7309711 7.03E-06 2.98E-06
vg0231634124 sf0231628255 2 31634124 NA 1.20E-06