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 mr1106 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
vg0217631846 sf0217625976 2 17631846 6.77E-09 3.50E-06
vg0216964105 sf0216958235 2 16964105 1.27E-08 2.21E-06
vg0323485018 sf0323483192 3 23485018 2.58E-08 2.93E-06
vg0131964524 sf0131963480 1 31964524 3.57E-07 1.25E-06
vg1216282324 sf1216279620 12 16282324 8.13E-06 NA
vg1013275525 sf1013204295 10 13275525 NA 1.37E-06
vg0526069160 sf0526006580 5 26069160 NA 1.46E-06
vg1122514350 sf1122048221 11 22514350 NA 1.78E-06
vg0323603573 sf0323601747 3 23603573 NA 2.32E-06