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 mr1110 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
vg0610566343 sf0610565344 6 10566343 1.40E-94 6.87E-35
vg0610071156 sf0610070157 6 10071156 8.62E-60 2.34E-17
vg0617621257 sf0617620260 6 17621257 7.04E-47 8.75E-07
vg0716061683 sf0716060690 7 16061683 2.30E-45 NA
vg0613070947 sf0613069948 6 13070947 2.81E-45 2.54E-06
vg0206646863 sf0206646863 2 6646863 8.65E-45 NA
vg0222647952 sf0222642083 2 22647952 2.08E-41 5.98E-08
vg0629122924 sf0629121926 6 29122924 8.62E-40 3.66E-07
vg0609920649 sf0609919650 6 9920649 NA 5.61E-15
vg0610444069 sf0610443070 6 10444069 NA 2.34E-11
vg0610808089 sf0610807090 6 10808089 NA 2.62E-11
vg0609697276 sf0609696277 6 9697276 NA 5.60E-11
vg0611127784 sf0611126785 6 11127784 NA 8.97E-11
vg0610587682 sf0610586683 6 10587682 NA 1.46E-09
vg0610143043 sf0610142044 6 10143043 NA 3.05E-09
vg0610020708 sf0610019709 6 10020708 NA 5.03E-09
vg0611682950 sf0611681951 6 11682950 NA 5.80E-09
vg0610281727 sf0610280728 6 10281727 NA 3.04E-08
vg0611723713 sf0611722714 6 11723713 NA 6.92E-08
vg0609643429 sf0609642430 6 9643429 NA 9.50E-08
vg1004031418 sf1004030394 10 4031418 NA 1.17E-07
vg0611818263 sf0611817264 6 11818263 NA 1.39E-07
vg1008968489 sf1008897350 10 8968489 NA 1.52E-07
vg1008810305 sf1008739167 10 8810305 NA 1.88E-07
vg0920308003 sf0920307522 9 20308003 NA 2.92E-07
vg1008348646 sf1008277508 10 8348646 NA 4.22E-07
vg0306622337 sf0306621337 3 6622337 NA 7.34E-07
vg1008504224 sf1008433086 10 8504224 NA 8.53E-07