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 mr1601 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
vg0805464731 sf0805463734 8 5464731 1.57E-44 2.58E-07
vg0820068882 sf0820066169 8 20068882 4.40E-44 1.71E-06
vg0626823814 sf0626822817 6 26823814 6.95E-44 NA
vg0624629287 sf0624628290 6 24629287 5.78E-43 4.95E-06
vg0916955985 sf0916954984 9 16955985 6.20E-43 NA
vg1218887444 sf1218858879 12 18887444 1.41E-42 8.51E-07
vg0826953770 sf0826951056 8 26953770 3.64E-42 5.42E-07
vg0720010188 sf0720009195 7 20010188 1.22E-41 1.39E-07
vg1214354909 sf1214352249 12 14354909 NA 1.49E-07
vg0719091461 sf0719090468 7 19091461 NA 5.42E-07
vg1124032771 sf1123566641 11 24032771 NA 7.73E-07
vg0114635543 sf0114634517 1 14635543 NA 1.54E-06
vg1217896822 sf1217868256 12 17896822 NA 1.80E-06