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 mr1918 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
vg0222725905 sf0222720036 2 22725905 4.06E-61 1.04E-54
vg0222739831 sf0222733962 2 22739831 3.09E-60 7.55E-56
vg0222725003 sf0222719134 2 22725003 1.44E-29 3.48E-21
vg0325231453 sf0325229534 3 25231453 2.49E-16 NA
vg0131785830 sf0131784786 1 31785830 5.62E-16 NA
vg0329368396 sf0329361436 3 29368396 5.92E-16 NA
vg0222730109 sf0222724240 2 22730109 1.80E-13 1.43E-08
vg0221957835 sf0221951966 2 21957835 2.02E-12 1.75E-06
vg0222730936 sf0222725067 2 22730936 4.36E-12 7.89E-08
vg0222817468 sf0222811599 2 22817468 NA 3.09E-11
vg0224664402 sf0224658533 2 24664402 NA 1.66E-08
vg0223663746 sf0223657877 2 23663746 NA 2.86E-08
vg0222802022 sf0222796153 2 22802022 NA 1.12E-07
vg0222729132 sf0222723263 2 22729132 NA 1.26E-07
vg0223663745 sf0223657876 2 23663745 NA 1.46E-07
vg0222686622 sf0222680753 2 22686622 NA 2.01E-07
vg0119929841 sf0119928796 1 19929841 NA 3.18E-07
vg0221650044 sf0221644175 2 21650044 NA 4.52E-07
vg0223747273 sf0223741404 2 23747273 NA 7.46E-07
vg0222702890 sf0222697021 2 22702890 NA 7.68E-07
vg0222041029 sf0222035160 2 22041029 NA 8.00E-07
vg0222842247 sf0222836378 2 22842247 NA 1.37E-06
vg0224878279 sf0224872410 2 24878279 NA 1.79E-06
vg0222663599 sf0222657730 2 22663599 NA 3.00E-06
vg0223169891 sf0223164022 2 23169891 NA 3.59E-06
vg0224242852 sf0224236983 2 24242852 NA 3.97E-06
vg0221590970 sf0221585101 2 21590970 NA 4.29E-06
vg0223792839 sf0223786970 2 23792839 NA 4.38E-06