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
vg0222739831 sf0222733962 2 22739831 1.08E-57 3.06E-51
vg0221701146 sf0221695277 2 21701146 6.11E-12 6.53E-08
vg0222730936 sf0222725067 2 22730936 7.23E-12 8.23E-07
vg0222854294 sf0222848425 2 22854294 8.85E-12 1.11E-11
vg0222879623 sf0222873754 2 22879623 2.16E-11 9.06E-13
vg0222730109 sf0222724240 2 22730109 2.57E-11 1.50E-07
vg0222765370 sf0222759501 2 22765370 4.85E-11 2.46E-06
vg0223641214 sf0223635345 2 23641214 1.61E-10 1.98E-09
vg0223077903 sf0223072034 2 23077903 3.40E-10 3.39E-07
vg0222799001 sf0222793132 2 22799001 3.79E-10 4.43E-07
vg0222729132 sf0222723263 2 22729132 3.58E-09 1.31E-06
vg0222624829 sf0222618960 2 22624829 6.53E-09 7.47E-10
vg0224802909 sf0224797040 2 24802909 1.18E-07 4.48E-06
vg0225207585 sf0225201716 2 25207585 1.38E-07 2.88E-06
vg0222857256 sf0222851387 2 22857256 4.13E-07 4.55E-06
vg0222674849 sf0222668980 2 22674849 1.12E-06 1.06E-07
vg0226490001 sf0226484132 2 26490001 2.61E-06 4.88E-06
vg0222686622 sf0222680753 2 22686622 8.31E-06 1.19E-06
vg0119929841 sf0119928796 1 19929841 NA 1.52E-06
vg1124072046 sf1123605916 11 24072046 NA 1.65E-06
vg0711810587 sf0711809593 7 11810587 NA 3.30E-06