| Variant ID: vg0724211176 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 24211176 |
| Reference Allele: T | Alternative Allele: TTG |
| Primary Allele: TTG | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 245. )
CTCCTCCGGGTAGAGCTAGATGCACCTGCTTTGCTCGCGCTGTGGTTACATGTGCCACGTTTCTCGTGTTCTTGATCGCTTCTCTGATCTTTCTCTCGTG[T/TTG]
TTTTTTTTCTCTCTTTTTTTTTCATTTCTCTTCGCGCGCGGAAACTGTTTCTTGTTACTCTTTTGATCCGGTCGCGTTTTTCTCTTTCACTTTTTATTTC
GAAATAAAAAGTGAAAGAGAAAAACGCGACCGGATCAAAAGAGTAACAAGAAACAGTTTCCGCGCGCGAAGAGAAATGAAAAAAAAAGAGAGAAAAAAAA[A/CAA]
CACGAGAGAAAGATCAGAGAAGCGATCAAGAACACGAGAAACGTGGCACATGTAACCACAGCGCGAGCAAAGCAGGTGCATCTAGCTCTACCCGGAGGAG
| Populations | Population Size | Frequency of TTG(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.20% | 43.30% | 0.47% | 0.00% | NA |
| All Indica | 2759 | 86.80% | 12.50% | 0.76% | 0.00% | NA |
| All Japonica | 1512 | 2.50% | 97.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 51.70% | 48.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 93.60% | 6.10% | 0.34% | 0.00% | NA |
| Indica II | 465 | 78.30% | 20.60% | 1.08% | 0.00% | NA |
| Indica III | 913 | 85.20% | 14.00% | 0.77% | 0.00% | NA |
| Indica Intermediate | 786 | 88.40% | 10.70% | 0.89% | 0.00% | NA |
| Temperate Japonica | 767 | 0.90% | 99.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 2.00% | 98.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 8.70% | 91.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 50.00% | 50.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 43.30% | 55.60% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0724211176 | T -> TTG | LOC_Os07g40370.1 | upstream_gene_variant ; 3212.0bp to feature; MODIFIER | silent_mutation | Average:64.002; most accessible tissue: Callus, score: 93.754 | N | N | N | N |
| vg0724211176 | T -> TTG | LOC_Os07g40390.1 | downstream_gene_variant ; 4701.0bp to feature; MODIFIER | silent_mutation | Average:64.002; most accessible tissue: Callus, score: 93.754 | N | N | N | N |
| vg0724211176 | T -> TTG | LOC_Os07g40380.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.002; most accessible tissue: Callus, score: 93.754 | N | N | N | N |