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 mr1191 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
vg1125555037 sf1125088876 11 25555037 1.01E-68 3.35E-46
vg1125583837 sf1125117676 11 25583837 1.15E-35 8.56E-28
vg0507714473 sf0507714414 5 7714473 1.40E-26 2.04E-13
vg1126473080 sf1126001494 11 26473080 7.00E-24 1.97E-14
vg1125148067 sf1124681907 11 25148067 1.41E-22 7.39E-15
vg0204430393 sf0204430390 2 4430393 2.64E-22 7.72E-11
vg1126527710 sf1126056125 11 26527710 4.44E-20 4.84E-15
vg1126515106 sf1126043521 11 26515106 1.43E-19 8.68E-12
vg1125504134 sf1125037973 11 25504134 1.74E-19 1.36E-12
vg1125878225 sf1125412144 11 25878225 1.15E-18 1.55E-10
vg0224605253 sf0224599384 2 24605253 2.81E-17 2.00E-12
vg1126030224 sf1125558638 11 26030224 4.02E-17 1.04E-09
vg1127281448 sf1126809835 11 27281448 8.60E-17 3.29E-10
vg1125162381 sf1124696221 11 25162381 8.85E-17 1.57E-09
vg1125602304 sf1125136143 11 25602304 1.11E-16 4.75E-21
vg1204321261 sf1204320249 12 4321261 7.91E-16 3.76E-09
vg0908554120 sf0908553119 9 8554120 1.29E-15 3.48E-10
vg1125862812 sf1125396731 11 25862812 6.58E-15 3.23E-12
vg1126312813 sf1125841226 11 26312813 8.18E-15 3.19E-09
vg1125782295 sf1125316134 11 25782295 3.53E-12 9.82E-18
vg1125261664 sf1124795504 11 25261664 2.10E-09 3.44E-09
vg0204429559 sf0204429556 2 4429559 3.07E-09 2.04E-10
vg1126252287 sf1125780701 11 26252287 NA 3.47E-06