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 mr1144 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
vg0610566084 sf0610565085 6 10566084 1.24E-52 1.39E-38
vg0610585046 sf0610584047 6 10585046 1.84E-18 2.75E-13
vg0610435285 sf0610434286 6 10435285 8.85E-18 1.16E-17
vg0610444061 sf0610443062 6 10444061 1.83E-16 1.70E-15
vg0920307704 sf0920307223 9 20307704 1.13E-15 1.53E-06
vg0610684949 sf0610683950 6 10684949 8.34E-15 9.59E-11
vg0610873460 sf0610872461 6 10873460 9.55E-15 3.66E-09
vg0610679932 sf0610678933 6 10679932 1.58E-14 4.12E-17
vg0610205289 sf0610204290 6 10205289 1.36E-12 1.50E-11
vg0611466166 sf0611465167 6 11466166 1.95E-12 3.45E-09
vg0610116533 sf0610115534 6 10116533 2.33E-12 2.14E-15
vg0610429643 sf0610428644 6 10429643 3.76E-12 3.17E-10
vg0611510915 sf0611509916 6 11510915 4.23E-12 4.15E-09
vg0610556004 sf0610555005 6 10556004 1.86E-11 2.07E-09
vg0610609111 sf0610608112 6 10609111 7.10E-11 1.94E-09
vg0615150907 sf0615149908 6 15150907 7.95E-11 9.75E-10
vg0610127588 sf0610126589 6 10127588 1.42E-09 7.92E-12
vg0611643367 sf0611642368 6 11643367 1.95E-08 1.27E-09
vg0610544169 sf0610543170 6 10544169 2.12E-08 4.91E-10
vg0612078079 sf0612077080 6 12078079 3.76E-08 1.47E-07
vg0610543789 sf0610542790 6 10543789 8.15E-08 3.72E-11
vg0413193204 sf0413183914 4 13193204 1.52E-07 NA
vg0618988041 sf0618987044 6 18988041 1.71E-07 6.60E-11
vg0516073587 sf0516016071 5 16073587 1.31E-06 NA
vg0610886531 sf0610885532 6 10886531 1.68E-06 5.43E-08
vg0613050715 sf0613049716 6 13050715 NA 3.56E-09
vg0611255073 sf0611254074 6 11255073 NA 4.08E-08
vg0617527186 sf0617526189 6 17527186 NA 7.57E-08