| Variant ID: vg0828406935 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 28406935 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATCCCCCTCAGACCGGTGGCTTACGTGAGGTAGAGGAGAGATTAGGTGGTAATTCTTGATTAATCCTCAATTGTCCAAGTACAGGGAAATATATGGCCCA[A/T]
TTGGCCAACAAACTAGGAAACAACTTATTCCTAAAATCTCTCCTAGCCACTTCCATCTACAGCCGCGGTGATCGCGGGCGCGGGCGCAGCTGCGTCGCGC
GCGCGACGCAGCTGCGCCCGCGCCCGCGATCACCGCGGCTGTAGATGGAAGTGGCTAGGAGAGATTTTAGGAATAAGTTGTTTCCTAGTTTGTTGGCCAA[T/A]
TGGGCCATATATTTCCCTGTACTTGGACAATTGAGGATTAATCAAGAATTACCACCTAATCTCTCCTCTACCTCACGTAAGCCACCGGTCTGAGGGGGAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.10% | 3.10% | 2.14% | 36.61% | NA |
| All Indica | 2759 | 42.30% | 0.10% | 1.88% | 55.67% | NA |
| All Japonica | 1512 | 77.00% | 9.30% | 2.91% | 10.78% | NA |
| Aus | 269 | 98.90% | 0.00% | 0.00% | 1.12% | NA |
| Indica I | 595 | 50.60% | 0.00% | 1.85% | 47.56% | NA |
| Indica II | 465 | 31.80% | 0.40% | 2.58% | 65.16% | NA |
| Indica III | 913 | 39.00% | 0.00% | 1.42% | 59.58% | NA |
| Indica Intermediate | 786 | 46.20% | 0.10% | 2.04% | 51.65% | NA |
| Temperate Japonica | 767 | 81.90% | 6.90% | 2.87% | 8.34% | NA |
| Tropical Japonica | 504 | 64.70% | 15.70% | 3.97% | 15.67% | NA |
| Japonica Intermediate | 241 | 87.10% | 3.70% | 0.83% | 8.30% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 1.04% | 2.08% | NA |
| Intermediate | 90 | 63.30% | 3.30% | 4.44% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0828406935 | A -> T | LOC_Os08g45240.3 | 3_prime_UTR_variant ; 363.0bp to feature; MODIFIER | silent_mutation | Average:14.961; most accessible tissue: Callus, score: 42.986 | N | N | N | N |
| vg0828406935 | A -> T | LOC_Os08g45240.2 | intron_variant ; MODIFIER | silent_mutation | Average:14.961; most accessible tissue: Callus, score: 42.986 | N | N | N | N |
| vg0828406935 | A -> T | LOC_Os08g45240.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.961; most accessible tissue: Callus, score: 42.986 | N | N | N | N |
| vg0828406935 | A -> T | LOC_Os08g45240.4 | intron_variant ; MODIFIER | silent_mutation | Average:14.961; most accessible tissue: Callus, score: 42.986 | N | N | N | N |
| vg0828406935 | A -> DEL | N | N | silent_mutation | Average:14.961; most accessible tissue: Callus, score: 42.986 | N | N | N | N |