| Variant ID: vg0123776036 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 23776036 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GAAGAACAGGGAGGAGAGAGGAGGGGAGGAGAAAAGGAGAAACGGAAAAAGACACACTAAATCACTGATCTCCCAAAACTATTGTGTGACCTAGACCTAG[T/C]
TGAGGTATTGCAGTCCTCGCCAATCTCCAAAGTGTGGCTTCTTCTGACATTGCCTTGGCGCCCTCAGTCCCGCTGCGTTGGCGGTGCTCGAATACTCTCA
TGAGAGTATTCGAGCACCGCCAACGCAGCGGGACTGAGGGCGCCAAGGCAATGTCAGAAGAAGCCACACTTTGGAGATTGGCGAGGACTGCAATACCTCA[A/G]
CTAGGTCTAGGTCACACAATAGTTTTGGGAGATCAGTGATTTAGTGTGTCTTTTTCCGTTTCTCCTTTTCTCCTCCCCTCCTCTCTCCTCCCTGTTCTTC
| 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 | 42.90% | 1.70% | 1.08% | 54.27% | NA |
| All Indica | 2759 | 11.20% | 0.00% | 1.67% | 87.06% | NA |
| All Japonica | 1512 | 87.20% | 5.20% | 0.20% | 7.41% | NA |
| Aus | 269 | 92.60% | 0.00% | 0.37% | 7.06% | NA |
| Indica I | 595 | 4.00% | 0.00% | 1.68% | 94.29% | NA |
| Indica II | 465 | 7.70% | 0.00% | 0.43% | 91.83% | NA |
| Indica III | 913 | 12.20% | 0.00% | 1.75% | 86.09% | NA |
| Indica Intermediate | 786 | 17.70% | 0.10% | 2.29% | 79.90% | NA |
| Temperate Japonica | 767 | 99.20% | 0.30% | 0.13% | 0.39% | NA |
| Tropical Japonica | 504 | 73.80% | 6.20% | 0.20% | 19.84% | NA |
| Japonica Intermediate | 241 | 76.80% | 19.10% | 0.41% | 3.73% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 63.30% | 1.10% | 1.11% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0123776036 | T -> DEL | N | N | silent_mutation | Average:13.914; most accessible tissue: Callus, score: 87.572 | N | N | N | N |
| vg0123776036 | T -> C | LOC_Os01g41930.1 | 5_prime_UTR_premature_start_codon_gain_variant ; LOW | silent_mutation | Average:13.914; most accessible tissue: Callus, score: 87.572 | N | N | N | N |
| vg0123776036 | T -> C | LOC_Os01g41930.1 | 5_prime_UTR_variant ; 466.0bp to feature; MODIFIER | silent_mutation | Average:13.914; most accessible tissue: Callus, score: 87.572 | N | N | N | N |
| vg0123776036 | T -> C | LOC_Os01g41920.1 | upstream_gene_variant ; 3353.0bp to feature; MODIFIER | silent_mutation | Average:13.914; most accessible tissue: Callus, score: 87.572 | N | N | N | N |
| vg0123776036 | T -> C | LOC_Os01g41910.1 | downstream_gene_variant ; 4521.0bp to feature; MODIFIER | silent_mutation | Average:13.914; most accessible tissue: Callus, score: 87.572 | N | N | N | N |