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 mr1213 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
vg0719090536 sf0719089543 7 19090536 3.57E-86 7.41E-45
vg0718904841 sf0718903848 7 18904841 3.18E-40 1.72E-07
vg0710656508 sf0710655514 7 10656508 4.17E-40 NA
vg0705653325 sf0705652326 7 5653325 3.02E-39 NA
vg0228211032 sf0228205163 2 28211032 2.13E-37 NA
vg0719397160 sf0719396167 7 19397160 3.22E-36 2.86E-07
vg0336383640 sf0336376510 3 36383640 2.21E-35 3.22E-07
vg0719057980 sf0719056987 7 19057980 NA 5.77E-29
vg0719071513 sf0719070520 7 19071513 NA 2.62E-23
vg0718865378 sf0718864385 7 18865378 NA 6.74E-21
vg0718922665 sf0718921672 7 18922665 NA 1.20E-13
vg0719413496 sf0719412503 7 19413496 NA 2.59E-12
vg0719105731 sf0719104738 7 19105731 NA 2.31E-11
vg0719044808 sf0719043815 7 19044808 NA 5.55E-11
vg0625175150 sf0625174153 6 25175150 NA 1.57E-07
vg0719449907 sf0719448914 7 19449907 NA 3.51E-07
vg0336251024 sf0336243894 3 36251024 NA 1.21E-06
vg0401784083 sf0401779679 4 1784083 NA 1.79E-06
vg0900606284 sf0900605284 9 606284 NA 1.95E-06
vg0421592157 sf0421420207 4 21592157 NA 1.98E-06
vg0418081728 sf0417909769 4 18081728 NA 2.66E-06
vg0719153643 sf0719152650 7 19153643 NA 2.97E-06
vg1116508452 sf1116043329 11 16508452 NA 3.01E-06
vg0419737874 sf0419565909 4 19737874 NA 4.26E-06