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 mr1847 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
vg0321576069 sf0321574579 3 21576069 6.06E-09 6.06E-09
vg0805946030 sf0805945033 8 5946030 7.56E-09 7.57E-09
vg0124420479 sf0124419435 1 24420479 8.85E-09 8.85E-09
vg0804905723 sf0804904726 8 4905723 1.42E-07 1.42E-07
vg0500776377 sf0500776359 5 776377 1.78E-07 1.78E-07
vg0329703696 sf0329696736 3 29703696 1.89E-07 1.89E-07
vg1020531763 sf1020460242 10 20531763 2.63E-07 2.63E-07
vg0222002131 sf0221996262 2 22002131 2.65E-07 2.65E-07
vg0138706549 sf0138705506 1 38706549 2.76E-07 2.76E-07
vg0218610196 sf0218604327 2 18610196 3.85E-07 3.85E-07
vg0900843849 sf0900842849 9 843849 4.56E-07 4.56E-07
vg0610852582 sf0610851583 6 10852582 4.74E-07 4.74E-07
vg0826077942 sf0826075228 8 26077942 4.84E-07 4.84E-07
vg1013161872 sf1013090643 10 13161872 8.93E-07 8.93E-07
vg1001247868 sf1001246845 10 1247868 1.02E-06 1.02E-06
vg0113510414 sf0113509388 1 13510414 1.26E-06 1.26E-06
vg0107079035 sf0107078035 1 7079035 1.48E-06 1.48E-06
vg0206578247 sf0206578247 2 6578247 1.80E-06 1.80E-06
vg0724377253 sf0724376259 7 24377253 1.86E-06 1.86E-06
vg0220356405 sf0220350537 2 20356405 2.00E-06 2.00E-06