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 mr1942 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
vg1214178574 sf1214175914 12 14178574 6.76E-20 4.52E-07
vg1214179429 sf1214176769 12 14179429 1.59E-19 2.26E-07
vg0423367176 sf0423182031 4 23367176 4.33E-17 NA
vg0726519355 sf0726518361 7 26519355 1.88E-16 NA
vg1018633254 sf1018561811 10 18633254 3.58E-16 NA
vg1211178169 sf1211175505 12 11178169 7.63E-16 NA
vg1215266864 sf1215264162 12 15266864 5.02E-15 1.71E-07
vg1215286899 sf1215284197 12 15286899 9.02E-14 5.30E-07
vg0310368348 sf0310367264 3 10368348 2.24E-11 9.78E-07
vg0805968808 sf0805967811 8 5968808 2.60E-10 2.67E-06
vg0315741484 sf0315740131 3 15741484 8.11E-10 NA
vg1204382817 sf1204381805 12 4382817 9.97E-10 4.96E-06
vg0906503065 sf0906502065 9 6503065 NA 2.20E-06
vg0228555399 sf0228549530 2 28555399 NA 4.23E-06