| Variant ID: vg1223325558 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 23325558 |
| Reference Allele: C | Alternative Allele: A,T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTTATACAAAGCCGTAGAAAGAACCCATGTTGAAATAGAATAGCCATGTTGCATTATACTCTAAAAATGCATATTCACTGGTTTACTTGTATTATTAATT[C/A,T]
CACCAGCATAATCTTCACCTTATTCAAGGCCCAAATCTAGAAAGTAGTCATGTTGAAATATAATAACAATATTATATTAAACTTGATTGATAGAAAAGTC
GACTTTTCTATCAATCAAGTTTAATATAATATTGTTATTATATTTCAACATGACTACTTTCTAGATTTGGGCCTTGAATAAGGTGAAGATTATGCTGGTG[G/T,A]
AATTAATAATACAAGTAAACCAGTGAATATGCATTTTTAGAGTATAATGCAACATGGCTATTCTATTTCAACATGGGTTCTTTCTACGGCTTTGTATAAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.20% | 0.00% | 0.00% | A: 0.13% |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.60% | 0.00% | 0.00% | 0.00% | A: 0.40% |
| Aus | 269 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.00% | A: 0.13% |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.00% | A: 0.20% |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 0.00% | A: 1.66% |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1223325558 | C -> A | LOC_Os12g37970.1 | 3_prime_UTR_variant ; 340.0bp to feature; MODIFIER | N | Average:59.336; most accessible tissue: Callus, score: 87.773 | N | N | N | N |
| vg1223325558 | C -> A | LOC_Os12g37970.2 | 3_prime_UTR_variant ; 340.0bp to feature; MODIFIER | N | Average:59.336; most accessible tissue: Callus, score: 87.773 | N | N | N | N |
| vg1223325558 | C -> A | LOC_Os12g37970.3 | 3_prime_UTR_variant ; 340.0bp to feature; MODIFIER | N | Average:59.336; most accessible tissue: Callus, score: 87.773 | N | N | N | N |
| vg1223325558 | C -> A | LOC_Os12g37960.1 | downstream_gene_variant ; 1805.0bp to feature; MODIFIER | N | Average:59.336; most accessible tissue: Callus, score: 87.773 | N | N | N | N |
| vg1223325558 | C -> A | LOC_Os12g37960.2 | downstream_gene_variant ; 1805.0bp to feature; MODIFIER | N | Average:59.336; most accessible tissue: Callus, score: 87.773 | N | N | N | N |
| vg1223325558 | C -> T | LOC_Os12g37970.1 | 3_prime_UTR_variant ; 340.0bp to feature; MODIFIER | N | Average:59.336; most accessible tissue: Callus, score: 87.773 | N | N | N | N |
| vg1223325558 | C -> T | LOC_Os12g37970.2 | 3_prime_UTR_variant ; 340.0bp to feature; MODIFIER | N | Average:59.336; most accessible tissue: Callus, score: 87.773 | N | N | N | N |
| vg1223325558 | C -> T | LOC_Os12g37970.3 | 3_prime_UTR_variant ; 340.0bp to feature; MODIFIER | N | Average:59.336; most accessible tissue: Callus, score: 87.773 | N | N | N | N |
| vg1223325558 | C -> T | LOC_Os12g37960.1 | downstream_gene_variant ; 1805.0bp to feature; MODIFIER | N | Average:59.336; most accessible tissue: Callus, score: 87.773 | N | N | N | N |
| vg1223325558 | C -> T | LOC_Os12g37960.2 | downstream_gene_variant ; 1805.0bp to feature; MODIFIER | N | Average:59.336; most accessible tissue: Callus, score: 87.773 | N | N | N | N |