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 mr1559 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
vg0216625467 sf0216619597 2 16625467 1.14E-21 1.76E-11
vg0216678835 sf0216672965 2 16678835 1.61E-16 3.16E-09
vg0622828231 sf0622827234 6 22828231 3.45E-12 NA
vg0907993257 sf0907992257 9 7993257 7.52E-12 NA
vg0917772044 sf0917771043 9 17772044 2.20E-11 NA
vg0216625325 sf0216619455 2 16625325 6.00E-10 2.19E-06
vg1218161842 sf1218133278 12 18161842 9.09E-09 NA
vg0423038839 sf0422853731 4 23038839 3.21E-08 2.58E-06
vg0221202711 sf0221196843 2 21202711 7.25E-08 1.66E-07
vg0327447631 sf0327440684 3 27447631 NA 3.30E-07
vg0729492205 sf0729491213 7 29492205 NA 2.08E-06
vg0207263344 sf0207263344 2 7263344 NA 2.22E-06
vg0820000696 sf0819997983 8 20000696 NA 2.74E-06
vg0327437336 sf0327430389 3 27437336 NA 3.76E-06
vg0401678473 sf0401674022 4 1678473 NA 4.32E-06
vg0523223119 sf0523160560 5 23223119 NA 4.38E-06