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 mr1024 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
vg1227357677 sf1227324077 12 27357677 2.30E-31 1.44E-06
vg0820977835 sf0820975122 8 20977835 4.49E-31 1.00E-06
vg0137882431 sf0137881388 1 37882431 1.01E-30 7.76E-06
vg1205730694 sf1205729676 12 5730694 1.25E-30 1.78E-06
vg1206809257 sf1206808147 12 6809257 2.37E-30 8.61E-09
vg0132865976 sf0132864932 1 32865976 8.76E-30 NA
vg1207149149 sf1207148039 12 7149149 NA 1.17E-07
vg0334733257 sf0334726127 3 34733257 NA 2.30E-07
vg1217936768 sf1217908202 12 17936768 NA 3.01E-07
vg1205372323 sf1205371309 12 5372323 NA 2.14E-06
vg0502226564 sf0502226539 5 2226564 NA 2.70E-06
vg0335235562 sf0335228431 3 35235562 NA 2.93E-06
vg1006588076 sf1006603699 10 6588076 NA 3.12E-06
vg1206760481 sf1206759371 12 6760481 NA 3.37E-06
vg0729406481 sf0729405489 7 29406481 NA 3.84E-06