| Variant ID: vg0121350172 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 21350172 |
| Reference Allele: TTCCGTCCTTATATATA | Alternative Allele: T,TGATCCGTCCTTATATATA |
| Primary Allele: TTCCGTCCTTATATATA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGGTTCTACTGCTGCGAGGCACAAGGTGCGTATAGTTGAAAAGAGTAAAAAGGTACACAACTGCAAAAATCAGCTCGGTCTACAACCGCTTAAAATTACG[TTCCGTCCTTATATATA/T,TGATCCGTCCTTATATATA]
GATTCATTTGTTTCTACCTTATTTCTCCCTCTGTTTTTTCTCTATTTGACATTGAACTAACCAACATCAGAAGTTTGGAAACATAGACATTATTAATTAT
ATAATTAATAATGTCTATGTTTCCAAACTTCTGATGTTGGTTAGTTCAATGTCAAATAGAGAAAAAACAGAGGGAGAAATAAGGTAGAAACAAATGAATC[TATATATAAGGACGGAA/A,TATATATAAGGACGGATCA]
CGTAATTTTAAGCGGTTGTAGACCGAGCTGATTTTTGCAGTTGTGTACCTTTTTACTCTTTTCAACTATACGCACCTTGTGCCTCGCAGCAGTAGAACCC
| Populations | Population Size | Frequency of TTCCGTCCTTATATATA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.70% | 1.30% | 0.00% | 0.00% | TGATCCGTCCTTATATATA: 0.02% |
| All Indica | 2759 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.20% | 3.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 96.60% | 3.40% | 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 | 97.90% | 1.00% | 0.00% | 0.00% | TGATCCGTCCTTATATATA: 1.04% |
| Intermediate | 90 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0121350172 | TTCCGTCCTTATATATA -> T | LOC_Os01g38120.1 | upstream_gene_variant ; 499.0bp to feature; MODIFIER | silent_mutation | Average:67.912; most accessible tissue: Zhenshan97 root, score: 79.452 | N | N | N | N |
| vg0121350172 | TTCCGTCCTTATATATA -> T | LOC_Os01g38140.1 | upstream_gene_variant ; 4297.0bp to feature; MODIFIER | silent_mutation | Average:67.912; most accessible tissue: Zhenshan97 root, score: 79.452 | N | N | N | N |
| vg0121350172 | TTCCGTCCTTATATATA -> T | LOC_Os01g38130.1 | intron_variant ; MODIFIER | silent_mutation | Average:67.912; most accessible tissue: Zhenshan97 root, score: 79.452 | N | N | N | N |
| vg0121350172 | TTCCGTCCTTATATATA -> TGATCCGTCCTTATATATA | LOC_Os01g38120.1 | upstream_gene_variant ; 499.0bp to feature; MODIFIER | silent_mutation | Average:67.912; most accessible tissue: Zhenshan97 root, score: 79.452 | N | N | N | N |
| vg0121350172 | TTCCGTCCTTATATATA -> TGATCCGTCCTTATATATA | LOC_Os01g38140.1 | upstream_gene_variant ; 4297.0bp to feature; MODIFIER | silent_mutation | Average:67.912; most accessible tissue: Zhenshan97 root, score: 79.452 | N | N | N | N |
| vg0121350172 | TTCCGTCCTTATATATA -> TGATCCGTCCTTATATATA | LOC_Os01g38130.1 | intron_variant ; MODIFIER | silent_mutation | Average:67.912; most accessible tissue: Zhenshan97 root, score: 79.452 | N | N | N | N |