| Variant ID: vg0823302212 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 23302212 |
| Reference Allele: GTATATATATATA | Alternative Allele: GTATATATA,GTATATA,GTATA,GTA,G |
| Primary Allele: GTATATATATATA | Secondary Allele: GTATA |
Inferred Ancestral Allele: Not determined.
TGCTAGGTGGTTTAAGACTCATGTAAGTGACGCACACTTACAAAAATATCATTTTTTGGTGATGAAATTTCAAATTGGGAATAACATGTGTATTTTTCTT[GTATATATATATA/GTATATATA,GTATATA,GTATA,GTA,G]
TATATATATATATATATATGACACTCATATGGGGCACCATGGTGCCCGGGCACCATGGTATCTAATGCACAAAATCACTCAAAGTTTTCAAAATTTCAAA
TTTGAAATTTTGAAAACTTTGAGTGATTTTGTGCATTAGATACCATGGTGCCCGGGCACCATGGTGCCCCATATGAGTGTCATATATATATATATATATA[TATATATATATAC/TATATATAC,TATATAC,TATAC,TAC,C]
AAGAAAAATACACATGTTATTCCCAATTTGAAATTTCATCACCAAAAAATGATATTTTTGTAAGTGTGCGTCACTTACATGAGTCTTAAACCACCTAGCA
| Populations | Population Size | Frequency of GTATATATATATA(primary allele) | Frequency of GTATA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 22.90% | 0.40% | 21.82% | 54.25% | GTATATA: 0.25%; GTATATATA: 0.13%; GTA: 0.11%; G: 0.08% |
| All Indica | 2759 | 1.60% | 0.00% | 12.87% | 85.43% | G: 0.07% |
| All Japonica | 1512 | 65.70% | 1.30% | 30.42% | 1.19% | GTATATA: 0.73%; GTATATATA: 0.40%; GTA: 0.26% |
| Aus | 269 | 3.30% | 0.40% | 50.56% | 45.35% | GTA: 0.37% |
| Indica I | 595 | 1.00% | 0.00% | 5.55% | 93.45% | NA |
| Indica II | 465 | 1.10% | 0.00% | 16.99% | 81.94% | NA |
| Indica III | 913 | 1.30% | 0.00% | 9.53% | 89.05% | G: 0.11% |
| Indica Intermediate | 786 | 2.80% | 0.00% | 19.85% | 77.23% | G: 0.13% |
| Temperate Japonica | 767 | 77.40% | 1.20% | 19.43% | 1.56% | GTA: 0.39% |
| Tropical Japonica | 504 | 51.20% | 1.60% | 43.85% | 0.60% | GTATATA: 1.59%; GTATATATA: 0.99%; GTA: 0.20% |
| Japonica Intermediate | 241 | 58.50% | 1.20% | 37.34% | 1.24% | GTATATA: 1.24%; GTATATATA: 0.41% |
| VI/Aromatic | 96 | 3.10% | 0.00% | 64.58% | 29.17% | G: 2.08%; GTATATA: 1.04% |
| Intermediate | 90 | 36.70% | 0.00% | 20.00% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0823302212 | GTATATATATATA -> GTATATATA | LOC_Os08g36870.1 | downstream_gene_variant ; 509.0bp to feature; MODIFIER | silent_mutation | Average:4.386; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0823302212 | GTATATATATATA -> GTATATATA | LOC_Os08g36880.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.386; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0823302212 | GTATATATATATA -> DEL | N | N | silent_mutation | Average:4.386; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0823302212 | GTATATATATATA -> GTATATA | LOC_Os08g36870.1 | downstream_gene_variant ; 507.0bp to feature; MODIFIER | silent_mutation | Average:4.386; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0823302212 | GTATATATATATA -> GTATATA | LOC_Os08g36880.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.386; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0823302212 | GTATATATATATA -> G | LOC_Os08g36870.1 | downstream_gene_variant ; 501.0bp to feature; MODIFIER | silent_mutation | Average:4.386; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0823302212 | GTATATATATATA -> G | LOC_Os08g36880.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.386; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0823302212 | GTATATATATATA -> GTA | LOC_Os08g36870.1 | downstream_gene_variant ; 503.0bp to feature; MODIFIER | silent_mutation | Average:4.386; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0823302212 | GTATATATATATA -> GTA | LOC_Os08g36880.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.386; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0823302212 | GTATATATATATA -> GTATA | LOC_Os08g36870.1 | downstream_gene_variant ; 505.0bp to feature; MODIFIER | silent_mutation | Average:4.386; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0823302212 | GTATATATATATA -> GTATA | LOC_Os08g36880.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.386; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |