| Variant ID: vg0629027181 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 29027181 |
| Reference Allele: CACGTCACG | Alternative Allele: C |
| Primary Allele: CACGTCACG | Secondary Allele: C |
Inferred Ancestral Allele : CACGTCACG (evidence from allele frequency in Oryza rufipogon: CACGTCACG: 1.00, others allele: 0.00, population size: 263. )
CCCAAATCCAAAAGGAAAGATTGCCATCTATCGCCCAATTGCCCTCCAAGAACATGCAACCTGCACAAGTGCAGAGGCCTGCATCCCCCTCGAGGTAGAT[CACGTCACG/C]
TCGCACGTGTGCAACGCATCGTGTGCCATGTCATCAGTTGGGGAACCTGCAGTCGCGGCGGATCTCGCCGCCGGTGGCCGGCGACTTGACGCCGACCCTG
CAGGGTCGGCGTCAAGTCGCCGGCCACCGGCGGCGAGATCCGCCGCGACTGCAGGTTCCCCAACTGATGACATGGCACACGATGCGTTGCACACGTGCGA[CGTGACGTG/G]
ATCTACCTCGAGGGGGATGCAGGCCTCTGCACTTGTGCAGGTTGCATGTTCTTGGAGGGCAATTGGGCGATAGATGGCAATCTTTCCTTTTGGATTTGGG
| Populations | Population Size | Frequency of CACGTCACG(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.20% | 0.50% | 8.34% | 0.99% | NA |
| All Indica | 2759 | 83.60% | 0.90% | 13.92% | 1.63% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.20% | 0.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.80% | 0.00% | 3.53% | 0.67% | NA |
| Indica II | 465 | 92.30% | 0.40% | 6.02% | 1.29% | NA |
| Indica III | 913 | 74.70% | 1.90% | 22.23% | 1.20% | NA |
| Indica Intermediate | 786 | 79.50% | 0.60% | 16.79% | 3.05% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.40% | 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 | 91.10% | 0.00% | 7.78% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0629027181 | CACGTCACG -> C | LOC_Os06g48010.1 | 3_prime_UTR_variant ; 34.0bp to feature; MODIFIER | silent_mutation | Average:66.63; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
| vg0629027181 | CACGTCACG -> C | LOC_Os06g48000.1 | downstream_gene_variant ; 3690.0bp to feature; MODIFIER | silent_mutation | Average:66.63; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
| vg0629027181 | CACGTCACG -> DEL | N | N | silent_mutation | Average:66.63; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |