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 mr1896 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
vg0524494561 sf0524431982 5 24494561 3.49E-113 2.05E-25
vg0524593054 sf0524530474 5 24593054 7.22E-111 2.18E-26
vg0917757454 sf0917756453 9 17757454 6.48E-76 NA
vg0411668128 sf0411658834 4 11668128 8.17E-76 NA
vg1021763384 sf1021691860 10 21763384 7.46E-75 NA
vg0408768585 sf0408763862 4 8768585 1.71E-74 NA
vg0524738001 sf0524675422 5 24738001 NA 4.28E-15
vg1100512559 sf1100511562 11 512559 NA 3.21E-07
vg0600226691 sf0600225691 6 226691 NA 3.70E-07
vg1205231921 sf1205230907 12 5231921 NA 4.13E-07
vg1122476819 sf1122010690 11 22476819 NA 8.21E-07
vg0800145551 sf0800144551 8 145551 NA 1.17E-06
vg0327131110 sf0327124163 3 27131110 NA 2.21E-06
vg0130667376 sf0130666332 1 30667376 NA 2.67E-06
vg1119055844 sf1118589532 11 19055844 NA 2.77E-06
vg1122487318 sf1122021189 11 22487318 NA 3.40E-06
vg1117053183 sf1116587035 11 17053183 NA 3.67E-06
vg0317014347 sf0317013221 3 17014347 NA 4.15E-06
vg0600909311 sf0600908312 6 909311 NA 4.20E-06
vg0917927607 sf0917926606 9 17927607 NA 5.38E-06
vg0521749530 sf0521686972 5 21749530 NA 6.25E-06