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 mr1972 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
vg1127568993 sf1127097380 11 27568993 4.45E-07 4.45E-07
vg1126306082 sf1125834495 11 26306082 5.60E-07 5.61E-07
vg1128742524 sf1128219303 11 28742524 7.20E-07 7.20E-07
vg0102110353 sf0102109353 1 2110353 1.68E-06 1.68E-06
vg0724583786 sf0724582792 7 24583786 1.91E-06 1.91E-06
vg0620778468 sf0620777471 6 20778468 1.94E-06 1.94E-06
vg0120143933 sf0120142888 1 20143933 2.45E-06 2.45E-06
vg0805963026 sf0805962029 8 5963026 2.67E-06 2.67E-06