| Variant ID: vg0420967601 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 20967601 |
| Reference Allele: AGTGT | Alternative Allele: A,AGT,AGTGTGT |
| Primary Allele: AGTGT | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCAGATCGTCCAGGGGCGCAGCGACGAGGAGGAAGGTGGGTGGGTGGGTGGCGCGCCCGATTTCGTGTTGCCCCCCCAATTTGCTGTCGGTTTATTTAAC[AGTGT/A,AGT,AGTGTGT]
GTGTGTGTGTGTGTTGTTTTTCTCTCCCTTGCGTTTCTGTGTGGGCAGAGGCTGGGCAGGACTGGCAGAAGGGGATTGTGGCGTCGTGCACCGAGTCGGA
TCCGACTCGGTGCACGACGCCACAATCCCCTTCTGCCAGTCCTGCCCAGCCTCTGCCCACACAGAAACGCAAGGGAGAGAAAAACAACACACACACACAC[ACACT/T,ACT,ACACACT]
GTTAAATAAACCGACAGCAAATTGGGGGGGCAACACGAAATCGGGCGCGCCACCCACCCACCCACCTTCCTCCTCGTCGCTGCGCCCCTGGACGATCTGC
| Populations | Population Size | Frequency of AGTGT(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.90% | 29.10% | 9.12% | 1.52% | AGT: 2.20%; AGTGTGT: 0.23% |
| All Indica | 2759 | 45.10% | 42.20% | 10.84% | 0.83% | AGT: 1.05% |
| All Japonica | 1512 | 85.80% | 0.50% | 7.01% | 3.04% | AGT: 2.91%; AGTGTGT: 0.66% |
| Aus | 269 | 27.10% | 68.40% | 3.35% | 0.00% | AGT: 0.74%; AGTGTGT: 0.37% |
| Indica I | 595 | 78.70% | 14.60% | 6.22% | 0.50% | NA |
| Indica II | 465 | 37.40% | 34.80% | 24.52% | 3.23% | NA |
| Indica III | 913 | 31.10% | 60.00% | 6.35% | 0.00% | AGT: 2.52% |
| Indica Intermediate | 786 | 40.60% | 46.60% | 11.45% | 0.64% | AGT: 0.76% |
| Temperate Japonica | 767 | 97.10% | 0.10% | 1.56% | 0.00% | AGT: 0.91%; AGTGTGT: 0.26% |
| Tropical Japonica | 504 | 76.40% | 1.00% | 8.53% | 7.54% | AGT: 5.95%; AGTGTGT: 0.60% |
| Japonica Intermediate | 241 | 69.70% | 0.80% | 21.16% | 3.32% | AGT: 2.90%; AGTGTGT: 2.07% |
| VI/Aromatic | 96 | 59.40% | 8.30% | 4.17% | 1.04% | AGT: 27.08% |
| Intermediate | 90 | 67.80% | 12.20% | 14.44% | 2.22% | AGT: 3.33% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420967601 | AGTGT -> DEL | N | N | silent_mutation | Average:54.359; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| vg0420967601 | AGTGT -> A | LOC_Os04g34650.1 | upstream_gene_variant ; 2934.0bp to feature; MODIFIER | silent_mutation | Average:54.359; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| vg0420967601 | AGTGT -> A | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.359; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| vg0420967601 | AGTGT -> AGT | LOC_Os04g34650.1 | upstream_gene_variant ; 2936.0bp to feature; MODIFIER | silent_mutation | Average:54.359; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| vg0420967601 | AGTGT -> AGT | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.359; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| vg0420967601 | AGTGT -> AGTGTGT | LOC_Os04g34650.1 | upstream_gene_variant ; 2938.0bp to feature; MODIFIER | silent_mutation | Average:54.359; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| vg0420967601 | AGTGT -> AGTGTGT | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.359; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |