| Variant ID: vg0804464111 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 4464111 |
| Reference Allele: C | Alternative Allele: CA,CAA,CAAA |
| Primary Allele: C | Secondary Allele: CA |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 105. )
ATAGGATGGAGGGACTAAGAAATTAATTCACAAACCATGGTAGCACTTTGCCTAATTTTGGGAAGAAAGGGTTGTGACATTCAGTTTTCTGTAGCAAGTA[C/CA,CAA,CAAA]
AAAAAAAAATCTTCAATGTTTGAAAAGCGTGTTCTTATCATTAACATGAACTACAGTTATTTGATGCAGCCCTGATTACCATTGTACACTTATTGGAGAA
TTCTCCAATAAGTGTACAATGGTAATCAGGGCTGCATCAAATAACTGTAGTTCATGTTAATGATAAGAACACGCTTTTCAAACATTGAAGATTTTTTTTT[G/TG,TTG,TTTG]
TACTTGCTACAGAAAACTGAATGTCACAACCCTTTCTTCCCAAAATTAGGCAAAGTGCTACCATGGTTTGTGAATTAATTTCTTAGTCCCTCCATCCTAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 25.10% | 7.90% | 1.04% | 65.81% | CAA: 0.17%; CAAA: 0.02% |
| All Indica | 2759 | 2.90% | 1.10% | 0.54% | 95.51% | CAA: 0.04% |
| All Japonica | 1512 | 71.20% | 21.40% | 1.98% | 4.96% | CAA: 0.33%; CAAA: 0.07% |
| Aus | 269 | 0.70% | 0.00% | 0.37% | 98.88% | NA |
| Indica I | 595 | 6.10% | 0.00% | 0.34% | 93.61% | NA |
| Indica II | 465 | 3.40% | 2.20% | 0.65% | 93.76% | NA |
| Indica III | 913 | 0.80% | 0.90% | 0.33% | 98.03% | NA |
| Indica Intermediate | 786 | 2.50% | 1.40% | 0.89% | 95.04% | CAA: 0.13% |
| Temperate Japonica | 767 | 77.30% | 16.80% | 3.52% | 1.69% | CAA: 0.65% |
| Tropical Japonica | 504 | 76.40% | 12.50% | 0.00% | 11.11% | NA |
| Japonica Intermediate | 241 | 41.10% | 54.80% | 1.24% | 2.49% | CAAA: 0.41% |
| VI/Aromatic | 96 | 2.10% | 9.40% | 1.04% | 85.42% | CAA: 2.08% |
| Intermediate | 90 | 26.70% | 13.30% | 2.22% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804464111 | C -> CAAA | LOC_Os08g07900.1 | upstream_gene_variant ; 3889.0bp to feature; MODIFIER | silent_mutation | Average:14.629; most accessible tissue: Callus, score: 60.841 | N | N | N | N |
| vg0804464111 | C -> CAAA | LOC_Os08g07910.1 | upstream_gene_variant ; 2991.0bp to feature; MODIFIER | silent_mutation | Average:14.629; most accessible tissue: Callus, score: 60.841 | N | N | N | N |
| vg0804464111 | C -> CAAA | LOC_Os08g07930.1 | upstream_gene_variant ; 1917.0bp to feature; MODIFIER | silent_mutation | Average:14.629; most accessible tissue: Callus, score: 60.841 | N | N | N | N |
| vg0804464111 | C -> CAAA | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.629; most accessible tissue: Callus, score: 60.841 | N | N | N | N |
| vg0804464111 | C -> CAA | LOC_Os08g07900.1 | upstream_gene_variant ; 3889.0bp to feature; MODIFIER | silent_mutation | Average:14.629; most accessible tissue: Callus, score: 60.841 | N | N | N | N |
| vg0804464111 | C -> CAA | LOC_Os08g07910.1 | upstream_gene_variant ; 2991.0bp to feature; MODIFIER | silent_mutation | Average:14.629; most accessible tissue: Callus, score: 60.841 | N | N | N | N |
| vg0804464111 | C -> CAA | LOC_Os08g07930.1 | upstream_gene_variant ; 1917.0bp to feature; MODIFIER | silent_mutation | Average:14.629; most accessible tissue: Callus, score: 60.841 | N | N | N | N |
| vg0804464111 | C -> CAA | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.629; most accessible tissue: Callus, score: 60.841 | N | N | N | N |
| vg0804464111 | C -> DEL | N | N | silent_mutation | Average:14.629; most accessible tissue: Callus, score: 60.841 | N | N | N | N |
| vg0804464111 | C -> CA | LOC_Os08g07900.1 | upstream_gene_variant ; 3889.0bp to feature; MODIFIER | silent_mutation | Average:14.629; most accessible tissue: Callus, score: 60.841 | N | N | N | N |
| vg0804464111 | C -> CA | LOC_Os08g07910.1 | upstream_gene_variant ; 2991.0bp to feature; MODIFIER | silent_mutation | Average:14.629; most accessible tissue: Callus, score: 60.841 | N | N | N | N |
| vg0804464111 | C -> CA | LOC_Os08g07930.1 | upstream_gene_variant ; 1917.0bp to feature; MODIFIER | silent_mutation | Average:14.629; most accessible tissue: Callus, score: 60.841 | N | N | N | N |
| vg0804464111 | C -> CA | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.629; most accessible tissue: Callus, score: 60.841 | N | N | N | N |