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 mr1083 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
vg0719067465 sf0719066472 7 19067465 5.11E-22 1.03E-19
vg0719006525 sf0719005532 7 19006525 5.44E-22 1.03E-19
vg1217490773 sf1217484728 12 17490773 4.95E-13 2.32E-08
vg0218614751 sf0218608882 2 18614751 1.30E-12 1.18E-07
vg0107198487 sf0107197487 1 7198487 1.55E-12 4.03E-08
vg1020494793 sf1020423272 10 20494793 5.57E-12 1.25E-08
vg0700416280 sf0700415280 7 416280 9.29E-12 6.11E-09
vg0218608139 sf0218602270 2 18608139 1.39E-11 5.21E-08
vg0113100532 sf0113099506 1 13100532 1.87E-11 9.38E-08
vg0627547379 sf0627546381 6 27547379 2.13E-11 2.62E-07
vg0417642687 sf0417470728 4 17642687 2.45E-11 9.43E-08
vg1100694812 sf1100693815 11 694812 3.38E-11 1.33E-08
vg0707738691 sf0707737696 7 7738691 3.94E-11 1.22E-08
vg1217240367 sf1217234322 12 17240367 5.72E-11 2.09E-08
vg1213429246 sf1213426584 12 13429246 4.47E-10 4.07E-07
vg0811122650 sf0811121655 8 11122650 6.08E-10 2.75E-09
vg0602041810 sf0602040811 6 2041810 1.08E-09 5.13E-07
vg0625303878 sf0625302881 6 25303878 2.95E-09 3.81E-07
vg0516162890 sf0516105374 5 16162890 4.38E-09 6.18E-08
vg0816277234 sf0816274520 8 16277234 8.04E-09 5.28E-07
vg0707873071 sf0707872076 7 7873071 1.31E-08 1.37E-06
vg0123426408 sf0123425364 1 23426408 1.63E-07 4.52E-07
vg0714249785 sf0714248792 7 14249785 3.85E-07 2.30E-07
vg0719049384 sf0719048391 7 19049384 5.70E-07 6.97E-14
vg0719056561 sf0719055568 7 19056561 1.54E-06 4.81E-14
vg0329561125 sf0329554165 3 29561125 NA 2.31E-07