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 mr1607 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
vg1215159630 sf1215156966 12 15159630 5.31E-14 NA
vg1215158192 sf1215155528 12 15158192 1.66E-13 NA
vg0322367512 sf0322366001 3 22367512 2.04E-11 NA
vg1215581638 sf1215578935 12 15581638 5.87E-11 NA
vg0723871939 sf0723870945 7 23871939 6.19E-11 8.62E-06
vg0920910881 sf0920910400 9 20910881 6.44E-11 NA
vg0808072179 sf0808071183 8 8072179 2.55E-09 8.39E-06
vg1222231033 sf1222197580 12 22231033 3.93E-09 NA
vg0724939108 sf0724938114 7 24939108 1.24E-08 NA
vg0229744763 sf0229738894 2 29744763 3.13E-08 NA
vg0232755756 sf0232749887 2 32755756 NA 2.52E-06
vg0909181183 sf0909180182 9 9181183 NA 2.91E-06
vg0611959824 sf0611958825 6 11959824 NA 4.39E-06