| Variant ID: vg0123775888 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 23775888 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATTGTAGAAAAATCTCAATGAGTGAAATAGCTTAGATCGTAAGAATACTCACAAATTAATGCATACCCTAGAGTTTTTTTTTTTGAAATACACAAAAGAC[T/C]
TGCATATCATTGCATTAAGAGGAGTAAAGTAATACAAGACAGACAGAGAAGAACAGGGAGGAGAGAGGAGGGGAGGAGAAAAGGAGAAACGGAAAAAGAC
GTCTTTTTCCGTTTCTCCTTTTCTCCTCCCCTCCTCTCTCCTCCCTGTTCTTCTCTGTCTGTCTTGTATTACTTTACTCCTCTTAATGCAATGATATGCA[A/G]
GTCTTTTGTGTATTTCAAAAAAAAAAACTCTAGGGTATGCATTAATTTGTGAGTATTCTTACGATCTAAGCTATTTCACTCATTGAGATTTTTCTACAAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 44.40% | 0.20% | 1.25% | 54.15% | NA |
| All Indica | 2759 | 11.20% | 0.10% | 2.10% | 86.63% | NA |
| All Japonica | 1512 | 92.00% | 0.30% | 0.00% | 7.74% | NA |
| Aus | 269 | 90.70% | 1.50% | 0.00% | 7.81% | NA |
| Indica I | 595 | 4.50% | 0.00% | 2.86% | 92.61% | NA |
| Indica II | 465 | 7.10% | 0.00% | 1.72% | 91.18% | NA |
| Indica III | 913 | 12.20% | 0.00% | 1.42% | 86.42% | NA |
| Indica Intermediate | 786 | 17.60% | 0.30% | 2.54% | 79.64% | NA |
| Temperate Japonica | 767 | 99.30% | 0.30% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 79.40% | 0.00% | 0.00% | 20.63% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.80% | 0.00% | 4.15% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 1.11% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0123775888 | T -> DEL | N | N | silent_mutation | Average:10.918; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775888 | T -> C | LOC_Os01g41930.1 | 5_prime_UTR_premature_start_codon_gain_variant ; LOW | silent_mutation | Average:10.918; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775888 | T -> C | LOC_Os01g41930.1 | 5_prime_UTR_variant ; 614.0bp to feature; MODIFIER | silent_mutation | Average:10.918; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775888 | T -> C | LOC_Os01g41920.1 | upstream_gene_variant ; 3205.0bp to feature; MODIFIER | silent_mutation | Average:10.918; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775888 | T -> C | LOC_Os01g41910.1 | downstream_gene_variant ; 4373.0bp to feature; MODIFIER | silent_mutation | Average:10.918; most accessible tissue: Callus, score: 62.341 | N | N | N | N |