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 mr1115 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
vg0908546508 sf0908545507 9 8546508 9.61E-10 2.14E-06
vg1117087408 sf1116621260 11 17087408 3.70E-09 8.56E-07
vg0908683598 sf0908682597 9 8683598 4.46E-09 NA
vg0136578944 sf0136577901 1 36578944 1.07E-08 9.25E-06
vg0138429641 sf0138428598 1 38429641 1.66E-08 NA
vg0908658415 sf0908657414 9 8658415 4.01E-07 NA
vg0922320585 sf0922320104 9 22320585 4.76E-07 NA
vg0210930737 sf0210930734 2 10930737 7.75E-07 8.32E-06
vg0508328858 sf0508328786 5 8328858 2.97E-06 2.34E-06
vg1202674747 sf1202673749 12 2674747 3.07E-06 1.74E-06