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 mr1067 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
vg0610564722 sf0610563723 6 10564722 3.85E-40 1.91E-23
vg0610558074 sf0610557075 6 10558074 6.51E-35 1.06E-25
vg0610584498 sf0610583499 6 10584498 1.87E-33 8.79E-20
vg0222727819 sf0222721950 2 22727819 1.59E-30 2.22E-19
vg0222725881 sf0222720012 2 22725881 3.89E-30 2.13E-21
vg0222733337 sf0222727468 2 22733337 2.17E-29 1.27E-20
vg0610412338 sf0610411339 6 10412338 2.27E-29 2.10E-15
vg0610609054 sf0610608055 6 10609054 1.64E-26 1.65E-14
vg0610680457 sf0610679458 6 10680457 2.14E-21 8.36E-16
vg0610471983 sf0610470984 6 10471983 3.16E-19 5.81E-10
vg0120607269 sf0120606224 1 20607269 7.82E-19 NA
vg0610147528 sf0610146529 6 10147528 1.13E-16 6.47E-10
vg0223747273 sf0223741404 2 23747273 2.67E-16 1.58E-08
vg0617779892 sf0617778895 6 17779892 7.17E-14 7.72E-07
vg0611292337 sf0611291338 6 11292337 1.29E-12 5.25E-08
vg0610608770 sf0610607771 6 10608770 4.16E-11 2.52E-07
vg0610696091 sf0610695092 6 10696091 NA 4.67E-12
vg0222654362 sf0222648493 2 22654362 NA 1.85E-10
vg0223043180 sf0223037311 2 23043180 NA 6.19E-09
vg0609638959 sf0609637960 6 9638959 NA 6.92E-09
vg0610442142 sf0610441143 6 10442142 NA 1.18E-08
vg0611079429 sf0611078430 6 11079429 NA 1.45E-08
vg0223048890 sf0223043021 2 23048890 NA 3.55E-08
vg0613809145 sf0613808146 6 13809145 NA 5.38E-08
vg0222557484 sf0222551615 2 22557484 NA 8.67E-08
vg0611636429 sf0611635430 6 11636429 NA 1.40E-07
vg0610379516 sf0610378517 6 10379516 NA 1.61E-07