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 mr1870 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
vg0715857906 sf0715856913 7 15857906 2.05E-30 NA
vg0719554891 sf0719553898 7 19554891 8.43E-25 NA
vg0705461791 sf0705460792 7 5461791 9.32E-25 NA
vg0230321839 sf0230315970 2 30321839 8.43E-24 NA
vg0100561383 sf0100560383 1 561383 9.23E-24 NA
vg0715874680 sf0715873687 7 15874680 1.58E-21 NA
vg0921456056 sf0921455575 9 21456056 NA 5.01E-09
vg1222847864 sf1222814303 12 22847864 NA 1.41E-06
vg1105881057 sf1105876809 11 5881057 NA 1.57E-06
vg0311687781 sf0311686499 3 11687781 NA 1.67E-06
vg0409481337 sf0409472035 4 9481337 NA 2.28E-06
vg1222433459 sf1222399898 12 22433459 NA 4.49E-06
vg1117628448 sf1117162304 11 17628448 NA 5.45E-06
vg0311656964 sf0311655682 3 11656964 NA 9.17E-06