| Variant ID: vg0302708596 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 2708596 |
| Reference Allele: T | Alternative Allele: TTAATTA,TTA |
| Primary Allele: T | Secondary Allele: TTAATTA |
Inferred Ancestral Allele: Not determined.
TGATCATGCAATCTCCATGCAAAGTATTGCTCTGAACAATAAATATTTCAGTAGCTCATGCCAGAGTTATGATGCTCATATTAATTAATTAATTAATTAA[T/TTAATTA,TTA]
ATAGGTGTCGTTGAATTCATTAAAAAATGTGGATGCGAATTTTTGTTTTCACCCTTTTCACTGCAAGAATTATCATCGTTATGTTTTTTCCCCACCTGGT
ACCAGGTGGGGAAAAAACATAACGATGATAATTCTTGCAGTGAAAAGGGTGAAAACAAAAATTCGCATCCACATTTTTTAATGAATTCAACGACACCTAT[A/TAATTAA,TAA]
TTAATTAATTAATTAATTAATATGAGCATCATAACTCTGGCATGAGCTACTGAAATATTTATTGTTCAGAGCAATACTTTGCATGGAGATTGCATGATCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TTAATTA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.10% | 0.15% | 0.00% | TTA: 0.04% |
| All Indica | 2759 | 99.70% | 0.10% | 0.18% | 0.00% | TTA: 0.04% |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.00% | TTA: 0.37% |
| Indica I | 595 | 99.50% | 0.20% | 0.17% | 0.00% | TTA: 0.17% |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.10% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0302708596 | T -> TTA | LOC_Os03g05480.1 | downstream_gene_variant ; 4716.0bp to feature; MODIFIER | N | Average:69.499; most accessible tissue: Minghui63 root, score: 89.19 | N | N | N | N |
| vg0302708596 | T -> TTA | LOC_Os03g05470.1 | intron_variant ; MODIFIER | N | Average:69.499; most accessible tissue: Minghui63 root, score: 89.19 | N | N | N | N |
| vg0302708596 | T -> TTAATTA | LOC_Os03g05480.1 | downstream_gene_variant ; 4716.0bp to feature; MODIFIER | N | Average:69.499; most accessible tissue: Minghui63 root, score: 89.19 | N | N | N | N |
| vg0302708596 | T -> TTAATTA | LOC_Os03g05470.1 | intron_variant ; MODIFIER | N | Average:69.499; most accessible tissue: Minghui63 root, score: 89.19 | N | N | N | N |