| Variant ID: vg0319757099 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 19757099 |
| Reference Allele: TG | Alternative Allele: T |
| Primary Allele: TG | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTTATTCGAGTGGTCGCTAATGAGGCAAGAACCATGGTTGTTGGTGGTATCATCATCATTAGTATTGCTAGTGTTGTTGTCTGCATTGCGTCCATCTTCT[TG/T]
GGGCAGGAACTCTTGATGCACAACAGAAGATCCGGTGATCTGAAGTGGCTCAGTGCGCTGTCTTTGGTTACCACATGGAAATACTGGGATGTTGACAATC
GATTGTCAACATCCCAGTATTTCCATGTGGTAACCAAAGACAGCGCACTGAGCCACTTCAGATCACCGGATCTTCTGTTGTGCATCAAGAGTTCCTGCCC[CA/A]
AGAAGATGGACGCAATGCAGACAACAACACTAGCAATACTAATGATGATGATACCACCAACAACCATGGTTCTTGCCTCATTAGCGACCACTCGAATAAA
| Populations | Population Size | Frequency of TG(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.50% | 0.20% | 3.87% | 62.44% | NA |
| All Indica | 2759 | 5.90% | 0.40% | 4.39% | 89.27% | NA |
| All Japonica | 1512 | 83.30% | 0.00% | 3.64% | 13.10% | NA |
| Aus | 269 | 13.00% | 0.00% | 0.37% | 86.62% | NA |
| Indica I | 595 | 4.40% | 0.00% | 2.02% | 93.61% | NA |
| Indica II | 465 | 5.20% | 0.60% | 3.66% | 90.54% | NA |
| Indica III | 913 | 5.90% | 0.90% | 7.01% | 86.20% | NA |
| Indica Intermediate | 786 | 7.60% | 0.00% | 3.56% | 88.80% | NA |
| Temperate Japonica | 767 | 94.30% | 0.00% | 1.17% | 4.56% | NA |
| Tropical Japonica | 504 | 65.70% | 0.00% | 6.75% | 27.58% | NA |
| Japonica Intermediate | 241 | 85.10% | 0.00% | 4.98% | 9.96% | NA |
| VI/Aromatic | 96 | 77.10% | 0.00% | 2.08% | 20.83% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 4.44% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319757099 | TG -> T | LOC_Os03g35670.1 | N | frameshift_variant | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0319757099 | TG -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |