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 mr1090 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
vg0610608095 sf0610607096 6 10608095 1.98E-41 4.85E-32
vg0610567030 sf0610566031 6 10567030 9.07E-40 4.66E-31
vg0610606146 sf0610605147 6 10606146 1.42E-39 3.78E-34
vg0610476418 sf0610475419 6 10476418 2.11E-25 1.84E-16
vg0610539571 sf0610538572 6 10539571 2.56E-25 1.34E-19
vg0610543653 sf0610542654 6 10543653 3.11E-23 4.77E-18
vg0610119624 sf0610118625 6 10119624 1.81E-20 1.37E-12
vg0610320030 sf0610319031 6 10320030 2.72E-20 1.34E-16
vg0610451701 sf0610450702 6 10451701 2.35E-19 1.75E-15
vg0610874933 sf0610873934 6 10874933 4.42E-17 9.36E-13
vg0610432373 sf0610431374 6 10432373 6.02E-13 1.18E-08
vg0613050715 sf0613049716 6 13050715 1.05E-12 7.15E-09
vg0617611502 sf0617610505 6 17611502 2.21E-12 3.71E-08
vg0610211069 sf0610210070 6 10211069 1.19E-11 8.43E-09
vg0611292337 sf0611291338 6 11292337 5.01E-11 3.58E-09
vg0610636368 sf0610635369 6 10636368 1.02E-10 2.18E-07
vg0610462543 sf0610461544 6 10462543 1.82E-10 2.04E-07
vg0611079429 sf0611078430 6 11079429 4.04E-10 3.16E-10
vg0610642256 sf0610641257 6 10642256 1.86E-09 1.68E-07
vg0613062563 sf0613061564 6 13062563 8.98E-08 4.73E-07
vg0611654043 sf0611653044 6 11654043 1.27E-07 1.54E-07
vg0610707156 sf0610706157 6 10707156 2.61E-07 7.73E-08
vg0610720006 sf0610719007 6 10720006 5.86E-07 3.99E-10
vg0421477298 sf0421305349 4 21477298 NA 1.39E-07
vg0124060154 sf0124059110 1 24060154 NA 3.57E-07