| Variant ID: vg0408179042 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 8179042 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TATTCTGGTTTGAGGGAGGAAATTCAGAACATTGTTGATTATAAGGAATTTAACTCTGTCAACAGTTGTTTCGGTTTGCTATGCTTGCAGAGAAGGAATT[A/G]
CAGGGGCGCGACCATCAGGGCAAGAGCAAGGCAAGCACATACACTCCGCGCACGACGCCATCTGCGGCACTGCCCAAGGCCGTCTCTTTTCGGGTGTCCT
AGGACACCCGAAAAGAGACGGCCTTGGGCAGTGCCGCAGATGGCGTCGTGCGCGGAGTGTATGTGCTTGCCTTGCTCTTGCCCTGATGGTCGCGCCCCTG[T/C]
AATTCCTTCTCTGCAAGCATAGCAAACCGAAACAACTGTTGACAGAGTTAAATTCCTTATAATCAACAATGTTCTGAATTTCCTCCCTCAAACCAGAATA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.70% | 2.10% | 3.64% | 27.51% | NA |
| All Indica | 2759 | 56.10% | 1.10% | 0.80% | 41.97% | NA |
| All Japonica | 1512 | 81.90% | 3.80% | 9.33% | 4.89% | NA |
| Aus | 269 | 78.40% | 0.40% | 0.74% | 20.45% | NA |
| Indica I | 595 | 48.40% | 0.30% | 0.34% | 50.92% | NA |
| Indica II | 465 | 66.20% | 2.20% | 1.51% | 30.11% | NA |
| Indica III | 913 | 56.30% | 0.50% | 0.77% | 42.39% | NA |
| Indica Intermediate | 786 | 55.70% | 1.80% | 0.76% | 41.73% | NA |
| Temperate Japonica | 767 | 97.80% | 0.30% | 0.65% | 1.30% | NA |
| Tropical Japonica | 504 | 58.10% | 9.50% | 22.22% | 10.12% | NA |
| Japonica Intermediate | 241 | 81.30% | 3.30% | 9.96% | 5.39% | NA |
| VI/Aromatic | 96 | 84.40% | 8.30% | 5.21% | 2.08% | NA |
| Intermediate | 90 | 83.30% | 2.20% | 2.22% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0408179042 | A -> DEL | LOC_Os04g14580.1 | N | frameshift_variant | Average:13.776; most accessible tissue: Callus, score: 35.853 | N | N | N | N |
| vg0408179042 | A -> G | LOC_Os04g14580.1 | synonymous_variant ; p.Leu211Leu; LOW | synonymous_codon | Average:13.776; most accessible tissue: Callus, score: 35.853 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0408179042 | NA | 4.22E-06 | mr1156 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0408179042 | 3.56E-06 | 9.46E-17 | mr1301 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0408179042 | NA | 7.53E-09 | mr1951 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0408179042 | 4.88E-07 | 9.50E-11 | mr1156_2 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0408179042 | NA | 5.56E-06 | mr1236_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0408179042 | NA | 3.59E-16 | mr1301_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0408179042 | NA | 3.96E-06 | mr1668_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |