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 mr1160 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
vg0921058093 sf0921057612 9 21058093 7.10E-07 7.10E-07
vg1224027002 sf1223993455 12 24027002 7.83E-07 7.81E-07
vg1224021705 sf1223988158 12 24021705 8.97E-07 8.95E-07
vg1112898481 sf1112434802 11 12898481 1.02E-06 1.02E-06
vg0512269844 sf0512269774 5 12269844 1.29E-06 1.29E-06
vg0511247093 sf0511247022 5 11247093 1.32E-06 1.32E-06
vg1122247251 sf1121781122 11 22247251 4.49E-06 4.48E-06
vg1127790110 sf1127318496 11 27790110 4.99E-06 4.99E-06