| Variant ID: vg0605309759 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 5309759 |
| Reference Allele: CT | Alternative Allele: CTT,C,CTTT |
| Primary Allele: CT | Secondary Allele: CTT |
Inferred Ancestral Allele: Not determined.
TGTCGCCTCATGATATATTGGATCTAGCGATGGCAATGGAGCCCCGTTGCCACCCCGGATTTGATCAGGTTATTTTCGGTGGTGTCATATGGTGTTTCAT[CT/CTT,C,CTTT]
TTTTTTTTTTAGTCTAGTATGGAAGATATGTACATGGCTTGTAGAGGGTGGCACCATGTAGTTTTGATGCCCTAGTCAAGTATCAGATGCATTAGTATTT
AAATACTAATGCATCTGATACTTGACTAGGGCATCAAAACTACATGGTGCCACCCTCTACAAGCCATGTACATATCTTCCATACTAGACTAAAAAAAAAA[AG/AAG,G,AAAG]
ATGAAACACCATATGACACCACCGAAAATAACCTGATCAAATCCGGGGTGGCAACGGGGCTCCATTGCCATCGCTAGATCCAATATATCATGAGGCGACA
| Populations | Population Size | Frequency of CT(primary allele) | Frequency of CTT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.60% | 9.00% | 1.16% | 0.00% | C: 2.22%; CTTT: 0.02% |
| All Indica | 2759 | 80.70% | 15.10% | 1.56% | 0.00% | C: 2.57%; CTTT: 0.04% |
| All Japonica | 1512 | 99.10% | 0.20% | 0.66% | 0.00% | C: 0.07% |
| Aus | 269 | 87.70% | 0.40% | 0.37% | 0.00% | C: 11.52% |
| Indica I | 595 | 68.20% | 27.90% | 3.70% | 0.00% | CTTT: 0.17% |
| Indica II | 465 | 98.30% | 0.40% | 0.22% | 0.00% | C: 1.08% |
| Indica III | 913 | 77.00% | 17.00% | 1.20% | 0.00% | C: 4.82% |
| Indica Intermediate | 786 | 84.10% | 12.00% | 1.15% | 0.00% | C: 2.80% |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.78% | 0.00% | C: 0.13% |
| Tropical Japonica | 504 | 98.80% | 0.60% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 3.30% | 1.11% | 0.00% | C: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0605309759 | CT -> C | LOC_Os06g10320.1 | downstream_gene_variant ; 3029.0bp to feature; MODIFIER | silent_mutation | Average:61.507; most accessible tissue: Callus, score: 82.241 | N | N | N | N |
| vg0605309759 | CT -> C | LOC_Os06g10330.1 | downstream_gene_variant ; 2013.0bp to feature; MODIFIER | silent_mutation | Average:61.507; most accessible tissue: Callus, score: 82.241 | N | N | N | N |
| vg0605309759 | CT -> C | LOC_Os06g10340.1 | intron_variant ; MODIFIER | silent_mutation | Average:61.507; most accessible tissue: Callus, score: 82.241 | N | N | N | N |
| vg0605309759 | CT -> CTT | LOC_Os06g10320.1 | downstream_gene_variant ; 3030.0bp to feature; MODIFIER | silent_mutation | Average:61.507; most accessible tissue: Callus, score: 82.241 | N | N | N | N |
| vg0605309759 | CT -> CTT | LOC_Os06g10330.1 | downstream_gene_variant ; 2014.0bp to feature; MODIFIER | silent_mutation | Average:61.507; most accessible tissue: Callus, score: 82.241 | N | N | N | N |
| vg0605309759 | CT -> CTT | LOC_Os06g10340.1 | intron_variant ; MODIFIER | silent_mutation | Average:61.507; most accessible tissue: Callus, score: 82.241 | N | N | N | N |
| vg0605309759 | CT -> CTTT | LOC_Os06g10320.1 | downstream_gene_variant ; 3030.0bp to feature; MODIFIER | silent_mutation | Average:61.507; most accessible tissue: Callus, score: 82.241 | N | N | N | N |
| vg0605309759 | CT -> CTTT | LOC_Os06g10330.1 | downstream_gene_variant ; 2014.0bp to feature; MODIFIER | silent_mutation | Average:61.507; most accessible tissue: Callus, score: 82.241 | N | N | N | N |
| vg0605309759 | CT -> CTTT | LOC_Os06g10340.1 | intron_variant ; MODIFIER | silent_mutation | Average:61.507; most accessible tissue: Callus, score: 82.241 | N | N | N | N |