| Variant ID: vg0629027073 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 29027073 |
| Reference Allele: G | Alternative Allele: GT |
| Primary Allele: GT | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 291. )
ATCGAACAAATCACTTTTACATCGTTGTATATTACAACTTATTCGGATCGTTGACAAAAACAACTTAAATTTTTGAACACACAATAATGTACTACCGATT[G/GT]
TTTTTTCCCCAAATCCAAAAGGAAAGATTGCCATCTATCGCCCAATTGCCCTCCAAGAACATGCAACCTGCACAAGTGCAGAGGCCTGCATCCCCCTCGA
TCGAGGGGGATGCAGGCCTCTGCACTTGTGCAGGTTGCATGTTCTTGGAGGGCAATTGGGCGATAGATGGCAATCTTTCCTTTTGGATTTGGGGAAAAAA[C/AC]
AATCGGTAGTACATTATTGTGTGTTCAAAAATTTAAGTTGTTTTTGTCAACGATCCGAATAAGTTGTAATATACAACGATGTAAAAGTGATTTGTTCGAT
| Populations | Population Size | Frequency of GT(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.20% | 36.90% | 7.66% | 2.24% | NA |
| All Indica | 2759 | 79.30% | 4.10% | 12.83% | 3.70% | NA |
| All Japonica | 1512 | 4.20% | 95.60% | 0.20% | 0.07% | NA |
| Aus | 269 | 44.60% | 55.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 86.70% | 9.20% | 2.69% | 1.34% | NA |
| Indica II | 465 | 89.20% | 2.80% | 6.45% | 1.51% | NA |
| Indica III | 913 | 73.90% | 1.00% | 21.14% | 3.94% | NA |
| Indica Intermediate | 786 | 74.20% | 4.70% | 14.63% | 6.49% | NA |
| Temperate Japonica | 767 | 2.90% | 96.90% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 6.20% | 93.50% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 4.10% | 95.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 56.70% | 34.40% | 5.56% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0629027073 | G -> DEL | N | N | silent_mutation | Average:63.73; most accessible tissue: Callus, score: 80.658 | N | N | N | N |
| vg0629027073 | G -> GT | LOC_Os06g48010.1 | 3_prime_UTR_variant ; 149.0bp to feature; MODIFIER | silent_mutation | Average:63.73; most accessible tissue: Callus, score: 80.658 | N | N | N | N |
| vg0629027073 | G -> GT | LOC_Os06g48000.1 | downstream_gene_variant ; 3582.0bp to feature; MODIFIER | silent_mutation | Average:63.73; most accessible tissue: Callus, score: 80.658 | N | N | N | N |