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 mr1765 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
vg0124310778 sf0124309734 1 24310778 3.55E-09 NA
vg1009832100 sf1009760921 10 9832100 9.81E-09 NA
vg0922372102 sf0922371621 9 22372102 1.12E-08 NA
vg0235115897 sf0235110028 2 35115897 2.37E-08 8.69E-07
vg0101292923 sf0101291923 1 1292923 3.26E-08 NA
vg0334827698 sf0334820568 3 34827698 1.35E-07 6.47E-07
vg0136552496 sf0136551453 1 36552496 6.40E-07 4.36E-06
vg0406038870 sf0406034309 4 6038870 1.76E-06 2.11E-06
vg0325685596 sf0325683614 3 25685596 2.67E-06 5.14E-06
vg0920840396 sf0920839915 9 20840396 4.94E-06 NA
vg0334986236 sf0334979106 3 34986236 5.82E-06 1.56E-06
vg0911232994 sf0911231993 9 11232994 7.43E-06 NA
vg0220855179 sf0220849311 2 20855179 NA 4.99E-06