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 mr1914 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
vg0217114921 sf0217109051 2 17114921 2.00E-64 6.04E-36
vg0217071746 sf0217065876 2 17071746 2.53E-63 1.51E-36
vg0217070481 sf0217064611 2 17070481 1.17E-41 1.77E-20
vg0217163428 sf0217157558 2 17163428 2.82E-41 4.92E-28
vg1015181696 sf1015110464 10 15181696 1.21E-25 1.98E-06
vg0217940995 sf0217935126 2 17940995 1.10E-24 1.56E-13
vg1220336354 sf1220307796 12 20336354 1.64E-24 1.26E-06
vg1128516527 sf1127993306 11 28516527 2.02E-20 2.11E-08
vg1108225523 sf1108220133 11 8225523 2.60E-20 5.79E-07
vg0217835710 sf0217829841 2 17835710 1.09E-16 2.50E-09
vg0217370560 sf0217364690 2 17370560 2.12E-16 4.53E-12
vg0217233564 sf0217227694 2 17233564 2.58E-15 2.18E-06
vg0217324370 sf0217318500 2 17324370 NA 1.09E-10
vg0217025287 sf0217019417 2 17025287 NA 2.19E-09
vg0217540070 sf0217534200 2 17540070 NA 3.83E-09
vg0218555416 sf0218549547 2 18555416 NA 5.35E-09
vg0217027791 sf0217021921 2 17027791 NA 2.16E-08
vg0218489541 sf0218483672 2 18489541 NA 6.90E-08
vg0217221174 sf0217215304 2 17221174 NA 1.68E-07
vg0212591710 sf0212591706 2 12591710 NA 2.79E-07
vg0215574189 sf0215568319 2 15574189 NA 3.27E-07
vg0708308206 sf0708307211 7 8308206 NA 1.83E-06
vg0315444805 sf0315443452 3 15444805 NA 3.44E-06