| Variant ID: vg0627801117 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 27801117 |
| Reference Allele: A | Alternative Allele: ACTCCCTCCG,ACTCCCTCCGT,ACTCCCTCCGTTTCGAAATGTTTGACGCCGT,ACTCCCTCCGTTTCGAAATGTTTGACGCCG |
| Primary Allele: A | Secondary Allele: ACTCCCTCCG |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 295. )
ATGATATACAGGCCGGATGGGTGGTAAGTGAACAACTAACCTTAATTGTCTATGTTAACATTTGGAGGATGTGTAGTACAATCAACATCAGCTATGATAT[A/ACTCCCTCCG,ACTCCCTCCGT,ACTCCCTCCGTTTCGAAATGTTTGACGCCGT,ACTCCCTCCGTTTCGAAATGTTTGACGCCG]
TATATCTCATCTCAAATGCTATTTTCCCTACATATATAGATTGATCCAACCACCTATGGTGACAGCAAAACCCACTTCTTTGTATCTTGGACGGTATGTG
CACATACCGTCCAAGATACAAAGAAGTGGGTTTTGCTGTCACCATAGGTGGTTGGATCAATCTATATATGTAGGGAAAATAGCATTTGAGATGAGATATA[T/CGGAGGGAGT,ACGGAGGGAGT,ACGGCGTCAAACATTTCGAAACGGAGGGAGT,CGGCGTCAAACATTTCGAAACGGAGGGAGT]
ATATCATAGCTGATGTTGATTGTACTACACATCCTCCAAATGTTAACATAGACAATTAAGGTTAGTTGTTCACTTACCACCCATCCGGCCTGTATATCAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of ACTCCCTCCG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.10% | 0.04% | 0.00% | ACTCCCTCCGTTTCGAAATGTTTGACGCCGT: 0.11%; ACTCCCTCCGT: 0.06%; ACTCCCTCCGTTTCGAAATGTTTGACGCCG: 0.02% |
| All Indica | 2759 | 99.40% | 0.20% | 0.07% | 0.00% | ACTCCCTCCGTTTCGAAATGTTTGACGCCGT: 0.18%; ACTCCCTCCGT: 0.11%; ACTCCCTCCGTTTCGAAATGTTTGACGCCG: 0.04% |
| All Japonica | 1512 | 100.00% | 0.00% | 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 | 98.60% | 0.50% | 0.00% | 0.00% | ACTCCCTCCGTTTCGAAATGTTTGACGCCGT: 0.55%; ACTCCCTCCGT: 0.22%; ACTCCCTCCGTTTCGAAATGTTTGACGCCG: 0.11% |
| Indica Intermediate | 786 | 99.60% | 0.00% | 0.25% | 0.00% | ACTCCCTCCGT: 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0627801117 | A -> ACTCCCTCCG | LOC_Os06g45910.1 | downstream_gene_variant ; 2538.0bp to feature; MODIFIER | N | Average:48.546; most accessible tissue: Callus, score: 67.738 | N | N | N | N |
| vg0627801117 | A -> ACTCCCTCCG | LOC_Os06g45920.1 | intron_variant ; MODIFIER | N | Average:48.546; most accessible tissue: Callus, score: 67.738 | N | N | N | N |
| vg0627801117 | A -> ACTCCCTCCGT | LOC_Os06g45910.1 | downstream_gene_variant ; 2538.0bp to feature; MODIFIER | N | Average:48.546; most accessible tissue: Callus, score: 67.738 | N | N | N | N |
| vg0627801117 | A -> ACTCCCTCCGT | LOC_Os06g45920.1 | intron_variant ; MODIFIER | N | Average:48.546; most accessible tissue: Callus, score: 67.738 | N | N | N | N |
| vg0627801117 | A -> ACTCCCTCCGTTTCGAAATGTTTGACGCCG T | LOC_Os06g45910.1 | downstream_gene_variant ; 2538.0bp to feature; MODIFIER | N | Average:48.546; most accessible tissue: Callus, score: 67.738 | N | N | N | N |
| vg0627801117 | A -> ACTCCCTCCGTTTCGAAATGTTTGACGCCG T | LOC_Os06g45920.1 | intron_variant ; MODIFIER | N | Average:48.546; most accessible tissue: Callus, score: 67.738 | N | N | N | N |
| vg0627801117 | A -> ACTCCCTCCGTTTCGAAATGTTTGACGCCG | LOC_Os06g45910.1 | downstream_gene_variant ; 2538.0bp to feature; MODIFIER | N | Average:48.546; most accessible tissue: Callus, score: 67.738 | N | N | N | N |
| vg0627801117 | A -> ACTCCCTCCGTTTCGAAATGTTTGACGCCG | LOC_Os06g45920.1 | intron_variant ; MODIFIER | N | Average:48.546; most accessible tissue: Callus, score: 67.738 | N | N | N | N |