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 mr1404 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
vg0719180192 sf0719179199 7 19180192 3.75E-23 1.47E-16
vg0719316520 sf0719315527 7 19316520 8.92E-23 1.90E-16
vg0719011406 sf0719010413 7 19011406 6.59E-21 7.28E-17
vg0719050776 sf0719049783 7 19050776 3.30E-16 4.84E-12
vg0718993983 sf0718992990 7 18993983 9.33E-15 2.74E-13
vg0719140447 sf0719139454 7 19140447 5.31E-11 8.43E-09
vg1201429922 sf1201428922 12 1429922 1.33E-10 1.78E-07
vg0717307582 sf0717306589 7 17307582 1.45E-10 4.93E-07
vg0719449907 sf0719448914 7 19449907 4.09E-10 1.74E-08
vg0719206073 sf0719205080 7 19206073 8.84E-09 1.12E-06
vg0235249589 sf0235243720 2 35249589 1.83E-08 3.66E-06
vg0429169933 sf0428984795 4 29169933 2.66E-08 1.29E-06
vg0222345805 sf0222339936 2 22345805 3.55E-07 4.44E-06
vg0222002361 sf0221996492 2 22002361 5.78E-07 4.92E-06
vg0718982442 sf0718981449 7 18982442 7.69E-07 2.39E-08
vg0408057944 sf0408053216 4 8057944 2.72E-06 4.16E-06
vg0414030990 sf0414021705 4 14030990 4.40E-06 1.25E-06
vg0319785500 sf0319784011 3 19785500 7.74E-06 2.79E-06
vg0228211068 sf0228205199 2 28211068 9.06E-06 2.25E-06
vg0407629243 sf0407624510 4 7629243 NA 5.30E-06