| Variant ID: vg0221167853 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 21167853 |
| Reference Allele: TA | Alternative Allele: T |
| Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTTGGATTGAATAAAATTTAGTGTGATCTTTCAACTAGTTTGGATGTGATGTTCTTGGTTGTTACTGTCTAACACCCTTATTGGTTATGTGCCACTTCAA[TA/T]
TTTTTTTTTTAATCTTTGTTACTCTGTTACCAATTATTTCACCCTTGACAATGTTTTGCTTGGCAGGTATTGTGTTGTTCTTGATGATATATGGAGTATT
AATACTCCATATATCATCAAGAACAACACAATACCTGCCAAGCAAAACATTGTCAAGGGTGAAATAATTGGTAACAGAGTAACAAAGATTAAAAAAAAAA[TA/A]
TTGAAGTGGCACATAACCAATAAGGGTGTTAGACAGTAACAACCAAGAACATCACATCCAAACTAGTTGAAAGATCACACTAAATTTTATTCAATCCAAA
| Populations | Population Size | Frequency of TA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.50% | 0.50% | 20.55% | 44.48% | NA |
| All Indica | 2759 | 6.30% | 0.00% | 27.26% | 66.47% | NA |
| All Japonica | 1512 | 90.30% | 1.60% | 4.83% | 3.31% | NA |
| Aus | 269 | 6.30% | 0.00% | 48.33% | 45.35% | NA |
| Indica I | 595 | 4.20% | 0.00% | 22.18% | 73.61% | NA |
| Indica II | 465 | 4.90% | 0.00% | 27.10% | 67.96% | NA |
| Indica III | 913 | 6.80% | 0.00% | 29.24% | 63.96% | NA |
| Indica Intermediate | 786 | 8.00% | 0.00% | 28.88% | 63.10% | NA |
| Temperate Japonica | 767 | 86.70% | 3.00% | 6.13% | 4.17% | NA |
| Tropical Japonica | 504 | 96.40% | 0.00% | 1.79% | 1.79% | NA |
| Japonica Intermediate | 241 | 88.80% | 0.40% | 7.05% | 3.73% | NA |
| VI/Aromatic | 96 | 27.10% | 0.00% | 4.17% | 68.75% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 13.33% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221167853 | TA -> T | LOC_Os02g35200.1 | downstream_gene_variant ; 2168.0bp to feature; MODIFIER | silent_mutation | Average:53.805; most accessible tissue: Minghui63 flag leaf, score: 73.752 | N | N | N | N |
| vg0221167853 | TA -> T | LOC_Os02g35220.1 | downstream_gene_variant ; 2675.0bp to feature; MODIFIER | silent_mutation | Average:53.805; most accessible tissue: Minghui63 flag leaf, score: 73.752 | N | N | N | N |
| vg0221167853 | TA -> T | LOC_Os02g35210.1 | intron_variant ; MODIFIER | silent_mutation | Average:53.805; most accessible tissue: Minghui63 flag leaf, score: 73.752 | N | N | N | N |
| vg0221167853 | TA -> DEL | N | N | silent_mutation | Average:53.805; most accessible tissue: Minghui63 flag leaf, score: 73.752 | N | N | N | N |