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 mr1926 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
vg1000458156 sf1000457132 10 458156 8.79E-90 2.65E-42
vg1000446805 sf1000445781 10 446805 1.39E-89 1.15E-43
vg1010987492 sf1010916312 10 10987492 3.69E-51 8.19E-11
vg1011111276 sf1011040096 10 11111276 4.91E-51 4.80E-11
vg0408443712 sf0408438986 4 8443712 6.22E-48 1.75E-07
vg0527042739 sf0526980095 5 27042739 4.56E-46 1.11E-06
vg1007820831 sf1007836441 10 7820831 1.26E-45 1.06E-06
vg0700359527 sf0700358527 7 359527 9.93E-44 3.55E-11
vg1125127481 sf1124661321 11 25127481 5.79E-43 8.51E-11
vg0528146502 sf0528083857 5 28146502 1.02E-41 2.59E-13
vg1125090609 sf1124624449 11 25090609 NA 7.62E-20
vg1001020612 sf1001019588 10 1020612 NA 1.22E-13
vg0129913271 sf0129912226 1 29913271 NA 7.56E-11
vg0328227704 sf0328220758 3 28227704 NA 8.79E-11
vg0528104538 sf0528041893 5 28104538 NA 1.98E-10
vg1008205459 sf1008134321 10 8205459 NA 2.46E-10
vg1001142065 sf1001141041 10 1142065 NA 3.00E-10
vg0210660828 sf0210660826 2 10660828 NA 7.71E-10
vg0328316154 sf0328309208 3 28316154 NA 9.11E-10
vg0607242294 sf0607241295 6 7242294 NA 1.11E-09
vg0307980063 sf0307979001 3 7980063 NA 1.48E-09
vg1122566432 sf1122100303 11 22566432 NA 1.61E-09
vg0611161418 sf0611160419 6 11161418 NA 1.62E-09
vg1122626801 sf1122160672 11 22626801 NA 3.01E-09
vg0330670598 sf0330663485 3 30670598 NA 3.31E-09
vg1000958635 sf1000957611 10 958635 NA 4.17E-09
vg1004952643 sf1004969180 10 4952643 NA 9.54E-09
vg1214648997 sf1214646337 12 14648997 NA 1.01E-08
vg1200149931 sf1200148931 12 149931 NA 1.07E-08
vg1000661364 sf1000660340 10 661364 NA 1.11E-08
vg1128800654 sf1128277433 11 28800654 NA 1.49E-08