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 mr1699 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
vg0107076753 sf0107075753 1 7076753 4.88E-46 3.19E-12
vg0121578906 sf0121577861 1 21578906 1.04E-42 5.00E-08
vg0212209606 sf0212209602 2 12209606 3.68E-41 NA
vg0825504763 sf0825502049 8 25504763 3.83E-41 NA
vg0827125579 sf0827122865 8 27125579 5.83E-41 2.63E-09
vg0821779217 sf0821776504 8 21779217 1.68E-40 9.94E-07
vg0821823829 sf0821821116 8 21823829 3.54E-40 4.63E-07
vg0323711509 sf0323709683 3 23711509 3.71E-40 2.02E-06
vg0426837648 sf0426652522 4 26837648 9.92E-39 5.00E-09
vg0313659201 sf0313657918 3 13659201 2.92E-37 1.13E-07
vg0915671665 sf0915670664 9 15671665 3.60E-36 2.21E-06
vg0501506459 sf0501506443 5 1506459 9.11E-31 3.24E-07
vg0102760349 sf0102759349 1 2760349 1.36E-29 1.91E-06
vg0107081316 sf0107080316 1 7081316 NA 9.28E-15
vg0331220750 sf0331213635 3 31220750 NA 4.84E-09
vg0331250575 sf0331243460 3 31250575 NA 7.84E-09
vg0821977951 sf0821975238 8 21977951 NA 2.15E-08
vg0107072026 sf0107071026 1 7072026 NA 8.16E-08
vg0823144076 sf0823141363 8 23144076 NA 9.93E-07
vg0234214663 sf0234208794 2 34214663 NA 1.03E-06
vg0910046361 sf0910045360 9 10046361 NA 1.26E-06
vg0819620862 sf0819618149 8 19620862 NA 1.34E-06
vg0724501205 sf0724500211 7 24501205 NA 1.81E-06
vg0724518323 sf0724517329 7 24518323 NA 2.23E-06
vg0107086714 sf0107085714 1 7086714 NA 2.31E-06
vg1104127107 sf1104123009 11 4127107 NA 2.40E-06
vg0825194810 sf0825192096 8 25194810 NA 3.50E-06
vg0219166982 sf0219161114 2 19166982 NA 3.74E-06
vg1104179321 sf1104175223 11 4179321 NA 5.64E-06
vg0825217312 sf0825214598 8 25217312 NA 9.41E-06