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 mr1042 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
vg0221812870 sf0221807001 2 21812870 2.49E-19 5.16E-14
vg0132071481 sf0132070437 1 32071481 4.55E-11 NA
vg0211187902 sf0211187899 2 11187902 2.25E-10 3.90E-06
vg0430557936 sf0430372811 4 30557936 5.09E-10 7.80E-07
vg1117878743 sf1117412600 11 17878743 5.37E-10 NA
vg0402662040 sf0402657644 4 2662040 1.31E-09 1.81E-06
vg0222002131 sf0221996262 2 22002131 1.35E-08 1.38E-06
vg0212053945 sf0212053941 2 12053945 1.42E-08 1.75E-06
vg0216185343 sf0216179473 2 16185343 3.62E-08 1.26E-06
vg0619160800 sf0619159803 6 19160800 5.47E-08 NA
vg0221815577 sf0221809708 2 21815577 NA 8.04E-08
vg0205347525 sf0205347525 2 5347525 NA 1.44E-06
vg0137044376 sf0137043333 1 37044376 NA 2.53E-06
vg0234417843 sf0234411974 2 34417843 NA 2.70E-06
vg1127358883 sf1126887270 11 27358883 NA 3.00E-06
vg1126133720 sf1125662134 11 26133720 NA 4.36E-06
vg0211188937 sf0211188934 2 11188937 NA 4.79E-06