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 mr1723 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
vg0333178922 sf0333171792 3 33178922 1.82E-22 4.65E-18
vg0333191872 sf0333184742 3 33191872 9.83E-22 1.48E-18
vg0333512189 sf0333505059 3 33512189 4.46E-10 5.23E-07
vg0333199277 sf0333192147 3 33199277 6.13E-10 8.00E-08
vg0333199495 sf0333192365 3 33199495 7.61E-10 5.92E-08
vg0332502505 sf0332495378 3 32502505 8.86E-10 1.74E-06
vg0332502161 sf0332495034 3 32502161 1.64E-09 1.49E-07
vg0333218322 sf0333211192 3 33218322 1.87E-09 2.68E-06
vg0332944170 sf0332937040 3 32944170 1.21E-08 3.92E-06
vg0333266499 sf0333259369 3 33266499 5.19E-07 8.31E-07
vg0122900476 sf0122899432 1 22900476 7.88E-07 4.91E-06
vg1215279207 sf1215276505 12 15279207 1.19E-06 NA