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 mr1912 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
vg0415621401 sf0415612088 4 15621401 1.74E-09 1.74E-09
vg0416188668 sf0416016701 4 16188668 1.66E-07 1.66E-07
vg0320879541 sf0320878051 3 20879541 3.56E-07 3.56E-07
vg0630585467 sf0630584469 6 30585467 4.35E-07 4.35E-07
vg0318338402 sf0318337184 3 18338402 5.80E-07 5.80E-07
vg0910260211 sf0910259210 9 10260211 7.59E-07 7.59E-07
vg0619422571 sf0619421574 6 19422571 1.90E-06 1.90E-06
vg0413811955 sf0413802671 4 13811955 2.09E-06 2.09E-06
vg0904007553 sf0904006553 9 4007553 4.10E-06 4.10E-06
vg0607387546 sf0607386547 6 7387546 4.16E-06 4.16E-06
vg1106425390 sf1106421142 11 6425390 4.26E-06 4.26E-06
vg0915089225 sf0915088224 9 15089225 4.28E-06 4.28E-06
vg1226021392 sf1225987786 12 26021392 4.96E-06 4.96E-06
vg0906460381 sf0906459381 9 6460381 9.18E-06 9.18E-06