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
vg0610676651 sf0610675652 6 10676651 1.49E-34 1.43E-16
vg0610584301 sf0610583302 6 10584301 1.65E-28 5.30E-13
vg0610459123 sf0610458124 6 10459123 7.59E-26 3.23E-18
vg0222727819 sf0222721950 2 22727819 2.19E-25 4.21E-15
vg0222729090 sf0222723221 2 22729090 4.35E-24 7.35E-16
vg0222738038 sf0222732169 2 22738038 1.85E-21 8.76E-15
vg0610609054 sf0610608055 6 10609054 6.47E-20 1.25E-07
vg0610808089 sf0610807090 6 10808089 1.67E-19 7.38E-11
vg0120651116 sf0120650071 1 20651116 3.11E-17 NA
vg0610450047 sf0610449048 6 10450047 9.86E-17 2.32E-09
vg0610683007 sf0610682008 6 10683007 5.89E-16 1.74E-11
vg0120461276 sf0120460231 1 20461276 4.11E-15 2.91E-06
vg0609930953 sf0609929954 6 9930953 5.86E-13 2.60E-08
vg0610875284 sf0610874285 6 10875284 7.75E-13 9.62E-08
vg0611952255 sf0611951256 6 11952255 2.30E-12 4.56E-07
vg0617810167 sf0617809170 6 17810167 4.55E-12 8.67E-07
vg0222671915 sf0222666046 2 22671915 NA 1.36E-08
vg0223688130 sf0223682261 2 23688130 NA 2.58E-08
vg0223077958 sf0223072089 2 23077958 NA 5.26E-08
vg1112908978 sf1112445299 11 12908978 NA 2.70E-07
vg0223033951 sf0223028082 2 23033951 NA 2.85E-07
vg0813088028 sf0813085658 8 13088028 NA 8.92E-07
vg0222316237 sf0222310368 2 22316237 NA 1.04E-06
vg0904658178 sf0904657178 9 4658178 NA 2.53E-06
vg1206658127 sf1206657017 12 6658127 NA 3.17E-06
vg0402263913 sf0402259508 4 2263913 NA 3.30E-06
vg0909224829 sf0909223828 9 9224829 NA 3.62E-06
vg1209714532 sf1209711941 12 9714532 NA 9.27E-06