| Variant ID: vg0727003263 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 27003263 |
| Reference Allele: A | Alternative Allele: ACTGAACATAGAGTCGAGC,ACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCGACT |
| Primary Allele: A | Secondary Allele: ACTGAACATAGAGTCGAGC |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 359. )
CTTGATGCTATAGAGGACCTCCAGAATAACCCTCAAGAACAAGAACCACACACATGGAGAGACATACAAAGCAGGTGGTGCATCGAACACCTTACTGAAA[A/ACTGAACATAGAGTCGAGC,ACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCGACT]
CTTATCTGCACATTTTGGTGGCAAGAAGTCGGCGGTGCTGTTCAATAAACTCTGTCAGCAGAGCCAACCAAGTAAGTTTACTGATATCTGGAAGGACCTA
TAGGTCCTTCCAGATATCAGTAAACTTACTTGGTTGGCTCTGCTGACAGAGTTTATTGAACAGCACCGCCGACTTCTTGCCACCAAAATGTGCAGATAAG[T/GCTCGACTCTATGTTCAGT,AGTCGGGGGCTACACAAATACAAGGCTCGACTCTATGTTCAGT]
TTTCAGTAAGGTGTTCGATGCACCACCTGCTTTGTATGTCTCTCCATGTGTGTGGTTCTTGTTCTTGAGGGTTATTCTGGAGGTCCTCTATAGCATCAAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of ACTGAACATAGAGTCGAGC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.60% | 0.10% | 0.21% | 0.00% | ACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCGACT: 0.11% |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 98.70% | 0.30% | 0.66% | 0.00% | ACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCGACT: 0.33% |
| 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.30% | 0.50% | 1.04% | 0.00% | ACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCGACT: 0.13% |
| Tropical Japonica | 504 | 98.80% | 0.20% | 0.20% | 0.00% | ACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCGACT: 0.79% |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0727003263 | A -> ACTGAACATAGAGTCGAGCCTTGTATTTGT GTAGCCCCCGACT | LOC_Os07g45250.1 | stop_gained&disruptive_inframe_insertion ; p.Asn400_Leu401insTerThrTerSer ArgAlaLeuTyrLeuCysSerProArgLeu; HIGH | N | Average:60.614; most accessible tissue: Callus, score: 87.142 | N | N | N | N |
| vg0727003263 | A -> ACTGAACATAGAGTCGAGCCTTGTATTTGT GTAGCCCCCGACT | LOC_Os07g45194.1 | upstream_gene_variant ; 2238.0bp to feature; MODIFIER | N | Average:60.614; most accessible tissue: Callus, score: 87.142 | N | N | N | N |
| vg0727003263 | A -> ACTGAACATAGAGTCGAGCCTTGTATTTGT GTAGCCCCCGACT | LOC_Os07g45260.1 | upstream_gene_variant ; 3359.0bp to feature; MODIFIER | N | Average:60.614; most accessible tissue: Callus, score: 87.142 | N | N | N | N |
| vg0727003263 | A -> ACTGAACATAGAGTCGAGC | LOC_Os07g45250.1 | stop_gained&disruptive_inframe_insertion ; p.Asn400_Leu401insTerThrTerSer ArgAla; HIGH | N | Average:60.614; most accessible tissue: Callus, score: 87.142 | N | N | N | N |
| vg0727003263 | A -> ACTGAACATAGAGTCGAGC | LOC_Os07g45194.1 | upstream_gene_variant ; 2238.0bp to feature; MODIFIER | N | Average:60.614; most accessible tissue: Callus, score: 87.142 | N | N | N | N |
| vg0727003263 | A -> ACTGAACATAGAGTCGAGC | LOC_Os07g45260.1 | upstream_gene_variant ; 3359.0bp to feature; MODIFIER | N | Average:60.614; most accessible tissue: Callus, score: 87.142 | N | N | N | N |