| Variant ID: vg1223325733 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 23325733 |
| Reference Allele: TG | Alternative Allele: T |
| Primary Allele: TG | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TATTAAACTTGATTGATAGAAAAGTCGCTAAGGAGATAGCTGGTTGTATTGTGAATACAGAGTGCCTTGCCCACTTGCATTGCATACATCAAGGACCAAG[TG/T]
GCAAAAGCTATCTTGCACACTAGCTAGATACATGAAACATGAGCACACTTGCAATGTTACATAGCTGTAAATATTTAGATCCATGCTAATGATTCTTCTA
TAGAAGAATCATTAGCATGGATCTAAATATTTACAGCTATGTAACATTGCAAGTGTGCTCATGTTTCATGTATCTAGCTAGTGTGCAAGATAGCTTTTGC[CA/A]
CTTGGTCCTTGATGTATGCAATGCAAGTGGGCAAGGCACTCTGTATTCACAATACAACCAGCTATCTCCTTAGCGACTTTTCTATCAATCAAGTTTAATA
| Populations | Population Size | Frequency of TG(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 85.40% | 14.60% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1223325733 | TG -> T | LOC_Os12g37970.1 | 3_prime_UTR_variant ; 164.0bp to feature; MODIFIER | silent_mutation | Average:67.073; most accessible tissue: Callus, score: 88.605 | N | N | N | N |
| vg1223325733 | TG -> T | LOC_Os12g37970.2 | 3_prime_UTR_variant ; 164.0bp to feature; MODIFIER | silent_mutation | Average:67.073; most accessible tissue: Callus, score: 88.605 | N | N | N | N |
| vg1223325733 | TG -> T | LOC_Os12g37970.3 | 3_prime_UTR_variant ; 164.0bp to feature; MODIFIER | silent_mutation | Average:67.073; most accessible tissue: Callus, score: 88.605 | N | N | N | N |
| vg1223325733 | TG -> T | LOC_Os12g37960.1 | downstream_gene_variant ; 1981.0bp to feature; MODIFIER | silent_mutation | Average:67.073; most accessible tissue: Callus, score: 88.605 | N | N | N | N |
| vg1223325733 | TG -> T | LOC_Os12g37960.2 | downstream_gene_variant ; 1981.0bp to feature; MODIFIER | silent_mutation | Average:67.073; most accessible tissue: Callus, score: 88.605 | N | N | N | N |