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 mr1274 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
vg0605274340 sf0605273341 6 5274340 3.06E-44 3.79E-26
vg0605311849 sf0605310850 6 5311849 2.88E-43 1.64E-26
vg0605335883 sf0605334884 6 5335883 7.50E-32 6.05E-15
vg0605162589 sf0605161590 6 5162589 8.77E-17 5.88E-09
vg0604727832 sf0604726833 6 4727832 3.05E-14 NA
vg0600826406 sf0600825407 6 826406 6.66E-14 NA
vg1104463006 sf1104458908 11 4463006 9.59E-14 2.78E-06
vg1104738557 sf1104734459 11 4738557 1.89E-13 2.54E-07
vg0604988139 sf0604987140 6 4988139 7.58E-13 4.57E-07
vg1104448760 sf1104444662 11 4448760 2.84E-12 3.92E-06
vg0918169636 sf0918168635 9 18169636 7.53E-12 1.86E-06
vg0605917767 sf0605916768 6 5917767 1.10E-11 8.48E-08
vg0604722110 sf0604721111 6 4722110 1.82E-11 4.60E-06
vg1010265444 sf1010194265 10 10265444 NA 2.28E-06
vg0604840256 sf0604839257 6 4840256 NA 3.69E-06