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 7.87E-93 1.50E-25
vg0205801196 sf0205801196 2 5801196 5.96E-61 NA
vg0230312250 sf0230306381 2 30312250 9.30E-60 NA
vg0708600682 sf0708599687 7 8600682 1.10E-59 NA
vg0304920678 sf0304919680 3 4920678 1.16E-59 NA
vg0314426110 sf0314424799 3 14426110 1.15E-54 3.65E-06
vg0402406368 sf0402401963 4 2406368 NA 2.34E-15
vg1010744278 sf1010673099 10 10744278 NA 4.48E-09
vg1010719593 sf1010648414 10 10719593 NA 1.73E-07
vg0402029490 sf0402025086 4 2029490 NA 6.33E-07
vg0207309711 sf0207309711 2 7309711 NA 6.70E-07
vg1017197950 sf1017126723 10 17197950 NA 1.10E-06
vg1008738737 sf1008667599 10 8738737 NA 1.13E-06
vg0402386328 sf0402381923 4 2386328 NA 1.94E-06
vg0427073206 sf0426888078 4 27073206 NA 2.74E-06
vg0401023314 sf0401018866 4 1023314 NA 2.89E-06
vg0230288040 sf0230282171 2 30288040 NA 3.40E-06
vg0229667121 sf0229661252 2 29667121 NA 3.68E-06
vg0522573546 sf0522510988 5 22573546 NA 4.87E-06
vg1122195477 sf1121729348 11 22195477 NA 5.96E-06