| Variant ID: vg0415575918 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15575918 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ACCTCCTCCCTCTCAGATCGATCTCTCTCCTCCTCCCCCTCCACCTCCTCCCCTTCCCATCCCATCCCCGGCCCTATCCTCCCCCTCCTCCCTTCCCACG[T/C]
GGGAGGTGGCCGGCTGGGCCGCGCACGGGCCCAGTGGCGAGCGGCGGCAGGCAGCAGCCGCTGCCGGCATCTTTTTTTTTTTTACAATTTGTGATTCACT
AGTGAATCACAAATTGTAAAAAAAAAAAAGATGCCGGCAGCGGCTGCTGCCTGCCGCCGCTCGCCACTGGGCCCGTGCGCGGCCCAGCCGGCCACCTCCC[A/G]
CGTGGGAAGGGAGGAGGGGGAGGATAGGGCCGGGGATGGGATGGGAAGGGGAGGAGGTGGAGGGGGAGGAGGAGAGAGATCGATCTGAGAGGGAGGAGGT
| 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 | 69.80% | 6.50% | 0.91% | 22.77% | NA |
| All Indica | 2759 | 71.50% | 11.10% | 0.76% | 16.64% | NA |
| All Japonica | 1512 | 76.70% | 0.00% | 1.32% | 22.02% | NA |
| Aus | 269 | 3.70% | 0.00% | 0.37% | 95.91% | NA |
| Indica I | 595 | 89.20% | 0.30% | 0.17% | 10.25% | NA |
| Indica II | 465 | 67.10% | 4.30% | 1.08% | 27.53% | NA |
| Indica III | 913 | 58.40% | 24.30% | 1.42% | 15.88% | NA |
| Indica Intermediate | 786 | 76.10% | 7.80% | 0.25% | 15.90% | NA |
| Temperate Japonica | 767 | 59.20% | 0.00% | 0.00% | 40.81% | NA |
| Tropical Japonica | 504 | 95.00% | 0.00% | 3.77% | 1.19% | NA |
| Japonica Intermediate | 241 | 93.80% | 0.00% | 0.41% | 5.81% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 0.00% | 9.38% | NA |
| Intermediate | 90 | 75.60% | 4.40% | 1.11% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575918 | T -> C | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:39.734; most accessible tissue: Zhenshan97 young leaf, score: 60.8 | N | N | N | N |
| vg0415575918 | T -> DEL | N | N | silent_mutation | Average:39.734; most accessible tissue: Zhenshan97 young leaf, score: 60.8 | N | N | N | N |