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 mr1696 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
vg0520178154 sf0520115627 5 20178154 2.64E-21 NA
vg0310907299 sf0310906017 3 10907299 6.30E-21 NA
vg0124347085 sf0124346041 1 24347085 1.00E-20 NA
vg0623849092 sf0623848095 6 23849092 2.65E-20 NA
vg0332021505 sf0332014382 3 32021505 1.42E-19 NA
vg0818186823 sf0818184110 8 18186823 1.97E-15 NA
vg0421984037 sf0421812088 4 21984037 3.43E-15 2.27E-06
vg1216321299 sf1216318595 12 16321299 3.20E-11 1.23E-07
vg0329517871 sf0329510911 3 29517871 8.89E-11 3.80E-07
vg1106187045 sf1106182797 11 6187045 1.08E-10 NA
vg0916156198 sf0916155197 9 16156198 1.74E-10 2.14E-07
vg0142339408 sf0142338364 1 42339408 NA 2.87E-07
vg0528518287 sf0528455642 5 28518287 NA 8.97E-07
vg1126391061 sf1125919474 11 26391061 NA 1.80E-06
vg1218228895 sf1218200331 12 18228895 NA 1.89E-06
vg0825492911 sf0825490197 8 25492911 NA 2.13E-06
vg0124441914 sf0124440870 1 24441914 NA 2.99E-06
vg0310942067 sf0310940785 3 10942067 NA 3.95E-06