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 mr1146 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
vg0222725905 sf0222720036 2 22725905 1.45E-33 6.03E-31
vg0223166694 sf0223160825 2 23166694 1.98E-09 5.57E-07
vg0223168818 sf0223162949 2 23168818 4.23E-09 3.76E-07
vg0224791922 sf0224786053 2 24791922 5.24E-09 2.49E-07
vg0224795001 sf0224789132 2 24795001 5.36E-09 2.46E-07
vg0222879623 sf0222873754 2 22879623 1.49E-08 8.16E-08
vg0222799001 sf0222793132 2 22799001 2.72E-08 1.96E-07
vg0222634177 sf0222628308 2 22634177 4.94E-08 3.89E-06
vg0222624829 sf0222618960 2 22624829 3.26E-07 8.21E-08
vg0222615084 sf0222609215 2 22615084 1.99E-06 3.77E-06
vg0224243811 sf0224237942 2 24243811 3.61E-06 2.78E-06
vg0400286523 sf0400285523 4 286523 6.35E-06 1.95E-06
vg0500226250 sf0500226250 5 226250 NA 3.71E-06