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 mr1585 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
vg0216957145 sf0216951275 2 16957145 3.94E-19 4.22E-08
vg0216974702 sf0216968832 2 16974702 4.71E-19 1.63E-08
vg1010636917 sf1010565738 10 10636917 1.02E-18 6.66E-09
vg1210106416 sf1210103827 12 10106416 8.32E-16 1.02E-06
vg0911265168 sf0911264167 9 11265168 1.74E-15 7.59E-07
vg0141700833 sf0141699790 1 41700833 1.99E-15 NA
vg0202715353 sf0202715351 2 2715353 6.21E-14 9.10E-08
vg0220269450 sf0220263582 2 20269450 4.19E-13 9.79E-08
vg0628047892 sf0628046894 6 28047892 5.46E-13 2.11E-07
vg0317023117 sf0317021991 3 17023117 1.31E-11 4.48E-11
vg1003132031 sf1003131008 10 3132031 4.63E-11 NA
vg0400995844 sf0400991396 4 995844 3.46E-10 2.41E-07
vg1005387575 sf1005404112 10 5387575 4.20E-10 1.81E-09
vg0327424324 sf0327417377 3 27424324 6.21E-10 5.46E-12
vg0327391604 sf0327384657 3 27391604 9.13E-10 2.45E-07
vg0327425445 sf0327418498 3 27425445 3.95E-09 9.65E-10
vg1009314607 sf1009243428 10 9314607 5.75E-09 NA
vg0324795678 sf0324793757 3 24795678 7.86E-09 5.66E-09
vg0222830353 sf0222824484 2 22830353 9.52E-09 8.26E-10
vg0327423375 sf0327416428 3 27423375 1.32E-08 1.98E-11
vg0622962887 sf0622961890 6 22962887 2.70E-08 2.29E-07
vg0907836758 sf0907835758 9 7836758 NA 2.76E-09
vg0719407633 sf0719406640 7 19407633 NA 4.45E-08
vg0304861604 sf0304860606 3 4861604 NA 8.71E-08
vg0314888685 sf0314887332 3 14888685 NA 1.17E-07
vg0308314436 sf0308313374 3 8314436 NA 1.40E-07
vg0628339348 sf0628338350 6 28339348 NA 2.47E-07
vg0229470684 sf0229464815 2 29470684 NA 2.73E-07
vg0308314268 sf0308313206 3 8314268 NA 6.30E-07