| Variant ID: vg0220738061 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 20738061 |
| Reference Allele: CA | Alternative Allele: TA,C |
| Primary Allele: CA | Secondary Allele: TA |
Inferred Ancestral Allele: Not determined.
CCAATCTAAACTAACTTATGTTCATACTACACTTGCCTTATTACCAATCTAAACTAACTAACACAAACTGGCCAGTTGCCCAGTTCCAACCGGCTACCAT[CA/TA,C]
ATATATTCCTAAAAACACCACTGAATTGTGTATCAATTTAATAAACATGGATTCATGGGTATTCACAAAGATGAGAGAAGCTTAAAGAATAACGACTTAC
GTAAGTCGTTATTCTTTAAGCTTCTCTCATCTTTGTGAATACCCATGAATCCATGTTTATTAAATTGATACACAATTCAGTGGTGTTTTTAGGAATATAT[TG/TA,G]
ATGGTAGCCGGTTGGAACTGGGCAACTGGCCAGTTTGTGTTAGTTAGTTTAGATTGGTAATAAGGCAAGTGTAGTATGAACATAAGTTAGTTTAGATTGG
| Populations | Population Size | Frequency of CA(primary allele) | Frequency of TA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.40% | 1.50% | 0.08% | 0.00% | C: 0.02% |
| All Indica | 2759 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.26% | 0.00% | C: 0.07% |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.52% | 0.00% | C: 0.13% |
| 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0220738061 | CA -> TA | LOC_Os02g34590.1 | 3_prime_UTR_variant ; 258.0bp to feature; MODIFIER | silent_mutation | Average:56.498; most accessible tissue: Callus, score: 82.569 | N | N | N | N |
| vg0220738061 | CA -> TA | LOC_Os02g34580.1 | downstream_gene_variant ; 730.0bp to feature; MODIFIER | silent_mutation | Average:56.498; most accessible tissue: Callus, score: 82.569 | N | N | N | N |
| vg0220738061 | CA -> C | LOC_Os02g34590.1 | 3_prime_UTR_variant ; 257.0bp to feature; MODIFIER | silent_mutation | Average:56.498; most accessible tissue: Callus, score: 82.569 | N | N | N | N |
| vg0220738061 | CA -> C | LOC_Os02g34580.1 | downstream_gene_variant ; 731.0bp to feature; MODIFIER | silent_mutation | Average:56.498; most accessible tissue: Callus, score: 82.569 | N | N | N | N |