| Variant ID: vg0128509376 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 28509376 |
| Reference Allele: T | Alternative Allele: G,TCAGAGC,TC |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TGAGATCACGGTTTCGTAGGAAGCGGTTCGCGCCGTTTTTCCCACGACACGCTCCTGTCAGGTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGACATA[T/G,TCAGAGC,TC]
ATGAACGATGGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGGCAGCGTCGGCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCC
GGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGCCGACGCTGCCCAGGTTCGGCCTAGACACCGCCACCATCACGCGCCTCCCATCGTTCAT[A/C,GCTCTGA,GA]
TATGTCACACCCCAATCTGGCACCGCCGTACAACGGCACCTGACAGGAGCGTGTCGTGGGAAAAACGGCGCGAACCGCTTCCTACGAAACCGTGATCTCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.60% | 0.20% | 8.74% | 52.41% | TCAGAGC: 0.04%; TC: 0.02% |
| All Indica | 2759 | 15.30% | 0.30% | 12.36% | 71.95% | TCAGAGC: 0.07%; TC: 0.04% |
| All Japonica | 1512 | 88.10% | 0.20% | 3.70% | 8.00% | NA |
| Aus | 269 | 4.10% | 0.00% | 2.23% | 93.68% | NA |
| Indica I | 595 | 6.40% | 0.20% | 6.05% | 87.39% | NA |
| Indica II | 465 | 9.90% | 0.00% | 5.16% | 84.95% | NA |
| Indica III | 913 | 27.30% | 0.70% | 22.02% | 49.84% | TCAGAGC: 0.22% |
| Indica Intermediate | 786 | 11.50% | 0.00% | 10.18% | 78.24% | TC: 0.13% |
| Temperate Japonica | 767 | 93.00% | 0.40% | 6.13% | 0.52% | NA |
| Tropical Japonica | 504 | 77.00% | 0.00% | 1.59% | 21.43% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 0.41% | 3.73% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 2.08% | 83.33% | NA |
| Intermediate | 90 | 47.80% | 0.00% | 8.89% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509376 | T -> G | LOC_Os01g49570.1 | synonymous_variant ; p.Ile66Ile; LOW | synonymous_codon | Average:21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128509376 | T -> TC | LOC_Os01g49570.1 | frameshift_variant ; p.Ile66fs; HIGH | frameshift_variant | Average:21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128509376 | T -> TCAGAGC | LOC_Os01g49570.1 | stop_gained&disruptive_inframe_insertion ; p.Ile66delinsMetLeuTer; HIGH | inframe_variant | Average:21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128509376 | T -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |