| Variant ID: vg0123776102 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 23776102 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GATCTCCCAAAACTATTGTGTGACCTAGACCTAGTTGAGGTATTGCAGTCCTCGCCAATCTCCAAAGTGTGGCTTCTTCTGACATTGCCTTGGCGCCCTC[A/T]
GTCCCGCTGCGTTGGCGGTGCTCGAATACTCTCAACCATTCCTTTCCTTCCAAATCGACCAAGCCCCGGGAACGATGATGGTATCGAACCCGCACCGTTG
CAACGGTGCGGGTTCGATACCATCATCGTTCCCGGGGCTTGGTCGATTTGGAAGGAAAGGAATGGTTGAGAGTATTCGAGCACCGCCAACGCAGCGGGAC[T/A]
GAGGGCGCCAAGGCAATGTCAGAAGAAGCCACACTTTGGAGATTGGCGAGGACTGCAATACCTCAACTAGGTCTAGGTCACACAATAGTTTTGGGAGATC
| 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 | 44.20% | 0.10% | 0.85% | 54.76% | NA |
| All Indica | 2759 | 10.80% | 0.30% | 1.20% | 87.71% | NA |
| All Japonica | 1512 | 92.10% | 0.00% | 0.13% | 7.74% | NA |
| Aus | 269 | 92.20% | 0.00% | 0.37% | 7.43% | NA |
| Indica I | 595 | 4.20% | 0.00% | 1.01% | 94.79% | NA |
| Indica II | 465 | 6.90% | 0.00% | 1.94% | 91.18% | NA |
| Indica III | 913 | 11.60% | 0.50% | 0.77% | 87.08% | NA |
| Indica Intermediate | 786 | 17.30% | 0.30% | 1.40% | 81.04% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.13% | 0.39% | NA |
| Tropical Japonica | 504 | 79.20% | 0.00% | 0.20% | 20.63% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 0.00% | 4.15% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 4.44% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0123776102 | A -> T | LOC_Os01g41930.1 | 5_prime_UTR_premature_start_codon_gain_variant ; LOW | silent_mutation | Average:12.935; most accessible tissue: Callus, score: 73.338 | N | N | N | N |
| vg0123776102 | A -> T | LOC_Os01g41930.1 | 5_prime_UTR_variant ; 400.0bp to feature; MODIFIER | silent_mutation | Average:12.935; most accessible tissue: Callus, score: 73.338 | N | N | N | N |
| vg0123776102 | A -> T | LOC_Os01g41920.1 | upstream_gene_variant ; 3419.0bp to feature; MODIFIER | silent_mutation | Average:12.935; most accessible tissue: Callus, score: 73.338 | N | N | N | N |
| vg0123776102 | A -> T | LOC_Os01g41910.1 | downstream_gene_variant ; 4587.0bp to feature; MODIFIER | silent_mutation | Average:12.935; most accessible tissue: Callus, score: 73.338 | N | N | N | N |
| vg0123776102 | A -> DEL | N | N | silent_mutation | Average:12.935; most accessible tissue: Callus, score: 73.338 | N | N | N | N |