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 mr1050 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
vg0330841186 sf0330834073 3 30841186 8.97E-16 3.46E-07
vg0920893174 sf0920892693 9 20893174 5.75E-15 NA
vg0920897668 sf0920897187 9 20897668 5.90E-15 NA
vg0330779142 sf0330772029 3 30779142 6.96E-15 1.09E-07
vg1018385481 sf1018314038 10 18385481 8.76E-13 NA
vg1104729203 sf1104725105 11 4729203 1.86E-12 NA
vg1221736592 sf1221703139 12 21736592 4.95E-12 4.50E-06
vg1213164297 sf1213161635 12 13164297 5.53E-10 NA
vg0213449877 sf0213449873 2 13449877 1.34E-09 NA
vg1005177676 sf1005194213 10 5177676 9.73E-09 NA
vg0106819630 sf0106818630 1 6819630 NA 4.63E-08
vg0211185461 sf0211185458 2 11185461 NA 1.91E-07
vg0808428148 sf0808427152 8 8428148 NA 4.14E-06
vg0521659473 sf0521596915 5 21659473 NA 4.51E-06
vg1206394265 sf1206393155 12 6394265 NA 5.27E-06