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 mr1586 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
vg1005695540 sf1005712078 10 5695540 8.09E-45 2.96E-11
vg1010636917 sf1010565738 10 10636917 1.82E-38 4.31E-10
vg0434705432 sf0434520321 4 34705432 1.70E-36 4.56E-07
vg1226954152 sf1226920551 12 26954152 5.15E-34 NA
vg0327439642 sf0327432695 3 27439642 5.21E-34 5.12E-12
vg0327391604 sf0327384657 3 27391604 7.45E-34 2.70E-10
vg1201753612 sf1201752609 12 1753612 2.37E-33 3.62E-08
vg0911246065 sf0911245064 9 11246065 3.80E-30 7.94E-10
vg0911039399 sf0911038398 9 11039399 1.47E-28 3.78E-08
vg0331362532 sf0331355417 3 31362532 1.90E-27 NA
vg0335000939 sf0334993809 3 35000939 3.93E-25 NA
vg0327424324 sf0327417377 3 27424324 NA 2.55E-19
vg0327425445 sf0327418498 3 27425445 NA 6.57E-18
vg1005967804 sf1005984342 10 5967804 NA 2.99E-15
vg0317023117 sf0317021991 3 17023117 NA 3.78E-15
vg0324795678 sf0324793757 3 24795678 NA 4.61E-15
vg0222830353 sf0222824484 2 22830353 NA 8.22E-13
vg1005694637 sf1005711175 10 5694637 NA 5.44E-12
vg0628001136 sf0628000138 6 28001136 NA 1.16E-11
vg0628049712 sf0628048714 6 28049712 NA 1.13E-10
vg0202735231 sf0202735229 2 2735231 NA 7.63E-10
vg0304861604 sf0304860606 3 4861604 NA 8.00E-10
vg0227637893 sf0227632024 2 27637893 NA 8.77E-10
vg0400468558 sf0400467556 4 468558 NA 8.88E-10
vg0222778846 sf0222772977 2 22778846 NA 1.02E-09
vg0907825976 sf0907824976 9 7825976 NA 1.27E-09
vg0220269450 sf0220263582 2 20269450 NA 2.66E-09
vg0628029397 sf0628028399 6 28029397 NA 3.69E-09
vg1009564247 sf1009493068 10 9564247 NA 5.02E-06