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 mr1565 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
vg0507480268 sf0507480210 5 7480268 2.06E-11 3.98E-10
vg0335027666 sf0335020536 3 35027666 2.21E-11 4.99E-08
vg0121102807 sf0121101762 1 21102807 2.08E-10 6.10E-07
vg0121172559 sf0121171514 1 21172559 2.77E-10 7.89E-08
vg0434580936 sf0434395828 4 34580936 2.98E-10 1.48E-07
vg0200274146 sf0200274146 2 274146 4.14E-10 2.50E-07
vg0618973254 sf0618972257 6 18973254 1.70E-09 1.26E-06
vg0401779398 sf0401774994 4 1779398 1.71E-09 1.88E-07
vg1207772422 sf1207769828 12 7772422 2.59E-09 1.14E-07
vg0912801939 sf0912800938 9 12801939 4.85E-09 2.29E-06
vg1206964772 sf1206963662 12 6964772 2.79E-08 1.58E-07
vg0620489670 sf0620488673 6 20489670 1.04E-07 2.57E-06
vg1215125172 sf1215122508 12 15125172 2.06E-07 1.50E-06
vg1206195784 sf1206194675 12 6195784 9.22E-06 1.88E-06
vg1014511015 sf1014439781 10 14511015 NA 1.73E-06