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 mr1232 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
vg1102677343 sf1102673247 11 2677343 1.07E-09 1.33E-07
vg1213717963 sf1213715301 12 13717963 1.27E-09 1.82E-08
vg0920272507 sf0920272026 9 20272507 4.39E-09 2.55E-07
vg0921699962 sf0921699481 9 21699962 4.70E-09 2.29E-07
vg1214863923 sf1214861264 12 14863923 2.45E-08 NA
vg0217857667 sf0217851798 2 17857667 3.28E-08 2.74E-06
vg0403315819 sf0403311422 4 3315819 3.58E-08 2.73E-07
vg0125628571 sf0125627527 1 25628571 3.77E-08 1.29E-06
vg0918918596 sf0918917596 9 18918596 4.24E-08 3.24E-06
vg1117567414 sf1117101270 11 17567414 5.68E-08 2.88E-06
vg0223262220 sf0223256351 2 23262220 1.86E-06 1.93E-06