| Variant ID: vg0114587391 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 14587391 |
| Reference Allele: CT | Alternative Allele: C,CTT,TT |
| Primary Allele: CT | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AAAATTCATTAATCAATTCTACTGCTTTATGCATAAAAATTGTTTAAGCATCTCAATGTATCAAATGTTAACCAAAACTAAACTGAAGCGGTTAAATAAG[CT/C,CTT,TT]
TTTTTTTTTATTGCTGAAGAGTACATTAATTTAAGTGTTGCATTCATGGTAAGAACAAGAACAACTATACAGAGTTTTTGTATGTACGAAGTTGAGTACT
AGTACTCAACTTCGTACATACAAAAACTCTGTATAGTTGTTCTTGTTCTTACCATGAATGCAACACTTAAATTAATGTACTCTTCAGCAATAAAAAAAAA[AG/G,AAG,AA]
CTTATTTAACCGCTTCAGTTTAGTTTTGGTTAACATTTGATACATTGAGATGCTTAAACAATTTTTATGCATAAAGCAGTAGAATTGATTAATGAATTTT
| 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 | 59.40% | 6.70% | 5.27% | 21.84% | CTT: 6.69%; TT: 0.02% |
| All Indica | 2759 | 37.50% | 11.10% | 8.59% | 36.82% | CTT: 5.91% |
| All Japonica | 1512 | 98.50% | 0.20% | 0.13% | 0.13% | CTT: 0.93%; TT: 0.07% |
| Aus | 269 | 48.00% | 1.90% | 0.74% | 0.00% | CTT: 49.44% |
| Indica I | 595 | 20.80% | 24.70% | 4.20% | 49.75% | CTT: 0.50% |
| Indica II | 465 | 35.30% | 18.10% | 16.34% | 30.32% | NA |
| Indica III | 913 | 46.50% | 0.90% | 7.56% | 33.84% | CTT: 11.17% |
| Indica Intermediate | 786 | 41.10% | 8.70% | 8.52% | 34.35% | CTT: 7.38% |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.00% | CTT: 0.13% |
| Tropical Japonica | 504 | 96.80% | 0.40% | 0.40% | 0.20% | CTT: 1.98%; TT: 0.20% |
| Japonica Intermediate | 241 | 97.90% | 0.40% | 0.00% | 0.41% | CTT: 1.24% |
| VI/Aromatic | 96 | 97.90% | 1.00% | 0.00% | 0.00% | CTT: 1.04% |
| Intermediate | 90 | 66.70% | 3.30% | 8.89% | 15.56% | CTT: 5.56% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114587391 | CT -> TT | LOC_Os01g25730.1 | downstream_gene_variant ; 4013.0bp to feature; MODIFIER | silent_mutation | Average:63.425; most accessible tissue: Zhenshan97 young leaf, score: 79.783 | N | N | N | N |
| vg0114587391 | CT -> TT | LOC_Os01g25740.1 | intron_variant ; MODIFIER | silent_mutation | Average:63.425; most accessible tissue: Zhenshan97 young leaf, score: 79.783 | N | N | N | N |
| vg0114587391 | CT -> CTT | LOC_Os01g25730.1 | downstream_gene_variant ; 4015.0bp to feature; MODIFIER | silent_mutation | Average:63.425; most accessible tissue: Zhenshan97 young leaf, score: 79.783 | N | N | N | N |
| vg0114587391 | CT -> CTT | LOC_Os01g25740.1 | intron_variant ; MODIFIER | silent_mutation | Average:63.425; most accessible tissue: Zhenshan97 young leaf, score: 79.783 | N | N | N | N |
| vg0114587391 | CT -> DEL | N | N | silent_mutation | Average:63.425; most accessible tissue: Zhenshan97 young leaf, score: 79.783 | N | N | N | N |
| vg0114587391 | CT -> C | LOC_Os01g25730.1 | downstream_gene_variant ; 4014.0bp to feature; MODIFIER | silent_mutation | Average:63.425; most accessible tissue: Zhenshan97 young leaf, score: 79.783 | N | N | N | N |
| vg0114587391 | CT -> C | LOC_Os01g25740.1 | intron_variant ; MODIFIER | silent_mutation | Average:63.425; most accessible tissue: Zhenshan97 young leaf, score: 79.783 | N | N | N | N |