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 mr1557 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
vg1102677343 sf1102673247 11 2677343 2.08E-10 9.20E-08
vg0921699962 sf0921699481 9 21699962 9.61E-10 3.33E-07
vg0125628571 sf0125627527 1 25628571 1.05E-09 1.09E-07
vg0920272507 sf0920272026 9 20272507 1.08E-09 1.83E-07
vg1115697103 sf1115233412 11 15697103 1.66E-09 NA
vg1213717963 sf1213715301 12 13717963 2.00E-09 1.27E-07
vg1213717956 sf1213715294 12 13717956 2.89E-09 1.32E-07
vg1117567414 sf1117101270 11 17567414 1.19E-08 3.21E-06
vg1003712007 sf1003710984 10 3712007 2.71E-06 NA