| Variant ID: vg0825985205 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 25985205 |
| Reference Allele: G | Alternative Allele: GCGCTTGTC,GC,GCGCTT |
| Primary Allele: G | Secondary Allele: GC |
Inferred Ancestral Allele: Not determined.
CCGGCACGCCGATGCGCAGGGAGACGTACTCGCCATTGTCCTCCTCGCGGTAGCCGCGCGGGTAGCATCTGATGACCCACGACTGCTCCCCGTCGCCGAC[G/GCGCTTGTC,GC,GCGCTT]
GCGAAGCTGTTCGTCGTCGTCGTCGTCCCTGGGTACTCGAGCTTCAACTCGGCGAAGCTGGATGATATCATCATCGTATTTTTGGTGTATTATTAATTAA
TTAATTAATAATACACCAAAAATACGATGATGATATCATCCAGCTTCGCCGAGTTGAAGCTCGAGTACCCAGGGACGACGACGACGACGAACAGCTTCGC[C/GACAAGCGC,GC,AAGCGC]
GTCGGCGACGGGGAGCAGTCGTGGGTCATCAGATGCTACCCGCGCGGCTACCGCGAGGAGGACAATGGCGAGTACGTCTCCCTGCGCATCGGCGTGCCGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.50% | 0.20% | 0.17% | 0.00% | GCGCTT: 0.06%; GCGCTTGTC: 0.04% |
| All Indica | 2759 | 99.30% | 0.30% | 0.29% | 0.00% | GCGCTT: 0.11% |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.90% | 0.70% | 0.00% | 0.00% | GCGCTTGTC: 0.37% |
| Indica I | 595 | 98.70% | 0.20% | 0.84% | 0.00% | GCGCTT: 0.34% |
| Indica II | 465 | 99.10% | 0.60% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.40% | 0.13% | 0.00% | GCGCTT: 0.13% |
| 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 | 98.90% | 0.00% | 0.00% | 0.00% | GCGCTTGTC: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0825985205 | G -> GCGCTTGTC | LOC_Os08g41120.1 | frameshift_variant ; p.Val26fs; HIGH | N | Average:81.06; most accessible tissue: Minghui63 young leaf, score: 88.629 | N | N | N | N |
| vg0825985205 | G -> GCGCTTGTC | LOC_Os08g41130.1 | upstream_gene_variant ; 3004.0bp to feature; MODIFIER | N | Average:81.06; most accessible tissue: Minghui63 young leaf, score: 88.629 | N | N | N | N |
| vg0825985205 | G -> GCGCTTGTC | LOC_Os08g41110.1 | downstream_gene_variant ; 1189.0bp to feature; MODIFIER | N | Average:81.06; most accessible tissue: Minghui63 young leaf, score: 88.629 | N | N | N | N |
| vg0825985205 | G -> GC | LOC_Os08g41120.1 | frameshift_variant ; p.Val26fs; HIGH | N | Average:81.06; most accessible tissue: Minghui63 young leaf, score: 88.629 | N | N | N | N |
| vg0825985205 | G -> GC | LOC_Os08g41130.1 | upstream_gene_variant ; 3004.0bp to feature; MODIFIER | N | Average:81.06; most accessible tissue: Minghui63 young leaf, score: 88.629 | N | N | N | N |
| vg0825985205 | G -> GC | LOC_Os08g41110.1 | downstream_gene_variant ; 1189.0bp to feature; MODIFIER | N | Average:81.06; most accessible tissue: Minghui63 young leaf, score: 88.629 | N | N | N | N |
| vg0825985205 | G -> GCGCTT | LOC_Os08g41120.1 | frameshift_variant ; p.Val26fs; HIGH | N | Average:81.06; most accessible tissue: Minghui63 young leaf, score: 88.629 | N | N | N | N |
| vg0825985205 | G -> GCGCTT | LOC_Os08g41130.1 | upstream_gene_variant ; 3004.0bp to feature; MODIFIER | N | Average:81.06; most accessible tissue: Minghui63 young leaf, score: 88.629 | N | N | N | N |