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 mr1267 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
vg0429780859 sf0429595728 4 29780859 2.93E-07 2.95E-07
vg0600102016 sf0600101016 6 102016 5.03E-07 5.05E-07
vg0105467815 sf0105466815 1 5467815 8.29E-07 8.31E-07
vg1209489380 sf1209486789 12 9489380 1.21E-06 1.22E-06
vg1127866165 sf1127394551 11 27866165 2.10E-06 2.11E-06
vg0432261918 sf0432076811 4 32261918 3.31E-06 3.33E-06
vg0518016012 sf0517955498 5 18016012 3.35E-06 3.36E-06
vg0422094587 sf0421941161 4 22094587 4.04E-06 4.06E-06
vg0426278854 sf0426093727 4 26278854 4.19E-06 4.22E-06
vg1218051198 sf1218022634 12 18051198 4.74E-06 4.74E-06
vg0114021291 sf0114020265 1 14021291 8.32E-06 8.36E-06