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 mr1330 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
vg0525516656 sf0525454077 5 25516656 1.23E-10 NA
vg0200277506 sf0200277506 2 277506 3.28E-10 NA
vg0140366212 sf0140365169 1 40366212 1.38E-09 NA
vg1102277267 sf1102273126 11 2277267 1.58E-09 NA
vg0907757405 sf0907756405 9 7757405 2.74E-09 NA
vg1121559924 sf1121093801 11 21559924 3.13E-07 9.55E-06
vg0114842613 sf0114841587 1 14842613 2.45E-06 NA
vg0805470240 sf0805469243 8 5470240 4.79E-06 7.02E-07
vg0103257998 sf0103256998 1 3257998 9.74E-06 NA