| Variant ID: vg0234180326 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 34180326 |
| Reference Allele: AC | Alternative Allele: A |
| Primary Allele: AC | Secondary Allele: A |
Inferred Ancestral Allele : AC (evidence from allele frequency in Oryza rufipogon: AC: 1.00, others allele: 0.00, population size: 340. )
GTCCCTGCAGCAGGTAAGAAAAAATTACAGTGGAGCAGAATTTGGGGCGGTTCATCTTCTAGCCATGGTGGTGGTACCAGTTCATCAGCAGCAAGTGGGG[AC/A]
GCTAGATCGCATGGTCCTGCCGAAGAGTTGTCCAACTATTTGGATAGCGATGCCATCAGGCATGAAACGTCAGACTTCAACGTACTCGGGTGGTGGAATG
CATTCCACCACCCGAGTACGTTGAAGTCTGACGTTTCATGCCTGATGGCATCGCTATCCAAATAGTTGGACAACTCTTCGGCAGGACCATGCGATCTAGC[GT/T]
CCCCACTTGCTGCTGATGAACTGGTACCACCACCATGGCTAGAAGATGAACCGCCCCAAATTCTGCTCCACTGTAATTTTTTCTTACCTGCTGCAGGGAC
| Populations | Population Size | Frequency of AC(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 71.70% | 0.10% | 11.81% | 16.42% | NA |
| All Indica | 2759 | 69.60% | 0.00% | 10.87% | 19.57% | NA |
| All Japonica | 1512 | 79.30% | 0.20% | 12.83% | 7.67% | NA |
| Aus | 269 | 59.10% | 0.00% | 15.99% | 24.91% | NA |
| Indica I | 595 | 57.30% | 0.00% | 27.39% | 15.29% | NA |
| Indica II | 465 | 61.10% | 0.00% | 7.31% | 31.61% | NA |
| Indica III | 913 | 83.70% | 0.00% | 3.83% | 12.49% | NA |
| Indica Intermediate | 786 | 67.40% | 0.00% | 8.65% | 23.92% | NA |
| Temperate Japonica | 767 | 75.10% | 0.00% | 18.25% | 6.65% | NA |
| Tropical Japonica | 504 | 85.30% | 0.60% | 5.95% | 8.13% | NA |
| Japonica Intermediate | 241 | 80.10% | 0.00% | 9.96% | 9.96% | NA |
| VI/Aromatic | 96 | 47.90% | 0.00% | 8.33% | 43.75% | NA |
| Intermediate | 90 | 73.30% | 0.00% | 14.44% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234180326 | AC -> A | LOC_Os02g55830.1 | frameshift_variant ; p.Asp436fs; HIGH | frameshift_variant | Average:9.274; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg0234180326 | AC -> DEL | LOC_Os02g55830.1 | N | frameshift_variant | Average:9.274; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |