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 mr1832 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
vg0805946030 sf0805945033 8 5946030 4.41E-09 4.41E-09
vg0321576069 sf0321574579 3 21576069 1.40E-08 1.40E-08
vg0124420479 sf0124419435 1 24420479 6.02E-08 6.02E-08
vg0329703696 sf0329696736 3 29703696 7.41E-08 7.41E-08
vg0826077942 sf0826075228 8 26077942 1.37E-07 1.37E-07
vg0206578247 sf0206578247 2 6578247 2.58E-07 2.58E-07
vg1013161872 sf1013090643 10 13161872 2.90E-07 2.90E-07
vg0138706549 sf0138705506 1 38706549 3.32E-07 3.32E-07
vg1020531763 sf1020460242 10 20531763 4.88E-07 4.88E-07
vg0218610196 sf0218604327 2 18610196 6.99E-07 6.99E-07
vg0500776377 sf0500776359 5 776377 1.08E-06 1.08E-06
vg0113510414 sf0113509388 1 13510414 1.21E-06 1.21E-06
vg0804905723 sf0804904726 8 4905723 1.25E-06 1.25E-06
vg0610852582 sf0610851583 6 10852582 1.44E-06 1.44E-06
vg1116613245 sf1116148123 11 16613245 1.55E-06 1.55E-06
vg0724377253 sf0724376259 7 24377253 1.64E-06 1.64E-06
vg0222002131 sf0221996262 2 22002131 1.67E-06 1.67E-06
vg1001247868 sf1001246845 10 1247868 1.99E-06 2.00E-06
vg0205924397 sf0205924397 2 5924397 2.38E-06 2.38E-06
vg0602731257 sf0602730258 6 2731257 2.76E-06 2.76E-06