| Variant ID: vg0426638588 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 26638588 |
| Reference Allele: CT | Alternative Allele: C,CTT |
| Primary Allele: CT | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AATTCACCGCGAATTTTGCAACTGCTGTACGCCTGAATGCATTGCACCTGTGTCCTGCTTCAAAACCCCCCTGTTTGCTTGTTGCTGCTCTCGTTTTTTT[CT/C,CTT]
TTTTTTTTTCAAATGCACCTTGATTTAAGGGAAGGGGAGAAGGGATTTTTTTTGTTTCCTACTATTTGCAAAGTGTTGTTCAGCTTCAGGACGATAGATG
CATCTATCGTCCTGAAGCTGAACAACACTTTGCAAATAGTAGGAAACAAAAAAAATCCCTTCTCCCCTTCCCTTAAATCAAGGTGCATTTGAAAAAAAAA[AG/G,AAG]
AAAAAAACGAGAGCAGCAACAAGCAAACAGGGGGGTTTTGAAGCAGGACACAGGTGCAATGCATTCAGGCGTACAGCAGTTGCAAAATTCGCGGTGAATT
| Populations | Population Size | Frequency of CT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.50% | 10.80% | 0.47% | 0.00% | CTT: 0.21% |
| All Indica | 2759 | 95.40% | 3.80% | 0.47% | 0.00% | CTT: 0.25% |
| All Japonica | 1512 | 74.10% | 25.30% | 0.53% | 0.00% | CTT: 0.07% |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.80% | 2.20% | 0.67% | 0.00% | CTT: 0.34% |
| Indica II | 465 | 97.40% | 2.20% | 0.43% | 0.00% | NA |
| Indica III | 913 | 93.40% | 6.60% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.50% | 2.90% | 0.89% | 0.00% | CTT: 0.64% |
| Temperate Japonica | 767 | 93.20% | 6.10% | 0.65% | 0.00% | NA |
| Tropical Japonica | 504 | 46.20% | 53.20% | 0.40% | 0.00% | CTT: 0.20% |
| Japonica Intermediate | 241 | 71.80% | 27.80% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 81.20% | 17.70% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 6.70% | 0.00% | 0.00% | CTT: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0426638588 | CT -> C | LOC_Os04g45030.1 | downstream_gene_variant ; 3582.0bp to feature; MODIFIER | silent_mutation | Average:61.545; most accessible tissue: Zhenshan97 flower, score: 80.904 | N | N | N | N |
| vg0426638588 | CT -> C | LOC_Os04g45020.1 | intron_variant ; MODIFIER | silent_mutation | Average:61.545; most accessible tissue: Zhenshan97 flower, score: 80.904 | N | N | N | N |
| vg0426638588 | CT -> CTT | LOC_Os04g45030.1 | downstream_gene_variant ; 3581.0bp to feature; MODIFIER | silent_mutation | Average:61.545; most accessible tissue: Zhenshan97 flower, score: 80.904 | N | N | N | N |
| vg0426638588 | CT -> CTT | LOC_Os04g45020.1 | intron_variant ; MODIFIER | silent_mutation | Average:61.545; most accessible tissue: Zhenshan97 flower, score: 80.904 | N | N | N | N |