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 mr1100 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
vg0222731119 sf0222725250 2 22731119 1.02E-15 2.91E-09
vg0222744532 sf0222738663 2 22744532 3.60E-15 2.13E-09
vg0120470627 sf0120469582 1 20470627 2.47E-11 5.85E-06
vg0223943227 sf0223937358 2 23943227 8.91E-11 NA
vg0201027436 sf0201027436 2 1027436 2.00E-09 NA
vg0402523133 sf0402518738 4 2523133 3.00E-09 5.25E-06
vg0222856459 sf0222850590 2 22856459 5.14E-09 7.28E-07
vg0406862446 sf0406857891 4 6862446 1.15E-08 5.21E-07
vg0612563052 sf0612562053 6 12563052 1.63E-08 4.78E-08
vg0618618072 sf0618617075 6 18618072 1.14E-07 1.39E-06
vg0406948268 sf0406943536 4 6948268 2.13E-07 NA
vg1205463941 sf1205462927 12 5463941 6.75E-07 3.68E-06
vg1219191852 sf1219163322 12 19191852 9.27E-07 NA
vg1215096314 sf1215093651 12 15096314 2.15E-06 NA
vg0706671410 sf0706670415 7 6671410 2.35E-06 4.87E-06
vg1012584019 sf1012512834 10 12584019 2.62E-06 6.21E-06
vg0827787589 sf0827784875 8 27787589 4.58E-06 3.64E-06
vg1001446321 sf1001445298 10 1446321 6.63E-06 NA
vg1226826332 sf1226792731 12 26826332 NA 1.07E-06
vg0132159113 sf0132158069 1 32159113 NA 3.29E-06
vg0407665649 sf0407660916 4 7665649 NA 3.35E-06