| Variant ID: vg0903405692 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr09 | Position: 3405692 |
| Reference Allele: TA | Alternative Allele: T |
| Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATTAACCAATGTCAGAAGACCTACAAATTTAACAAATGATAAATATGATCCCCATGGTTTTGATATAACCTCTACTGATTTTTTAGGATTAAAACACAAA[TA/T]
AAGAAAAAACAAACTTTCCACAATACATCAATCAAAGAAACATATATGCGTATTTCCACATATGAGTTCAATTCCAACAGAACTTTTGAAAGATATGTAC
GTACATATCTTTCAAAAGTTCTGTTGGAATTGAACTCATATGTGGAAATACGCATATATGTTTCTTTGATTGATGTATTGTGGAAAGTTTGTTTTTTCTT[TA/A]
TTTGTGTTTTAATCCTAAAAAATCAGTAGAGGTTATATCAAAACCATGGGGATCATATTTATCATTTGTTAAATTTGTAGGTCTTCTGACATTGGTTAAT
| 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 | 92.50% | 7.50% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 95.30% | 4.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 18.60% | 81.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 92.00% | 8.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0903405692 | TA -> T | LOC_Os09g07010.1 | upstream_gene_variant ; 2584.0bp to feature; MODIFIER | silent_mutation | Average:48.859; most accessible tissue: Callus, score: 77.599 | N | N | N | N |
| vg0903405692 | TA -> T | LOC_Os09g07030.1 | downstream_gene_variant ; 3187.0bp to feature; MODIFIER | silent_mutation | Average:48.859; most accessible tissue: Callus, score: 77.599 | N | N | N | N |
| vg0903405692 | TA -> T | LOC_Os09g07020.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.859; most accessible tissue: Callus, score: 77.599 | N | N | N | N |
| vg0903405692 | TA -> T | LOC_Os09g07020.2 | intron_variant ; MODIFIER | silent_mutation | Average:48.859; most accessible tissue: Callus, score: 77.599 | N | N | N | N |