| Variant ID: vg0804463121 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 4463121 |
| Reference Allele: GT | Alternative Allele: GTT,G |
| Primary Allele: GT | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GAATTAAAATTCGTATTTGATCCTAGATAGATATAGCAGATGCTTACATGGTCTAAGTAACATTCTTTGATAAGGTTTAATGCATATAAATATTGCATCA[GT/GTT,G]
TTTTTTTTAAAAAAAAAATTCTTCAATTGTTGTGATATATGCGCCCCAACCGATTTGAACTCTCAATGTAGGACTAATATATTCCCGGGTATTATGTTCA
TGAACATAATACCCGGGAATATATTAGTCCTACATTGAGAGTTCAAATCGGTTGGGGCGCATATATCACAACAATTGAAGAATTTTTTTTTTAAAAAAAA[AC/AAC,C]
TGATGCAATATTTATATGCATTAAACCTTATCAAAGAATGTTACTTAGACCATGTAAGCATCTGCTATATCTATCTAGGATCAAATACGAATTTTAATTC
| Populations | Population Size | Frequency of GT(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 24.10% | 9.10% | 0.87% | 65.83% | GTT: 0.11% |
| All Indica | 2759 | 3.40% | 0.50% | 0.40% | 95.65% | NA |
| All Japonica | 1512 | 66.90% | 26.30% | 1.59% | 4.96% | GTT: 0.20% |
| Aus | 269 | 1.10% | 0.40% | 1.49% | 97.03% | NA |
| Indica I | 595 | 6.10% | 0.00% | 0.34% | 93.61% | NA |
| Indica II | 465 | 3.40% | 1.90% | 0.43% | 94.19% | NA |
| Indica III | 913 | 1.00% | 0.00% | 0.22% | 98.80% | NA |
| Indica Intermediate | 786 | 4.30% | 0.60% | 0.64% | 94.40% | NA |
| Temperate Japonica | 767 | 70.40% | 25.00% | 2.74% | 1.56% | GTT: 0.26% |
| Tropical Japonica | 504 | 72.40% | 15.90% | 0.20% | 11.31% | GTT: 0.20% |
| Japonica Intermediate | 241 | 44.40% | 52.30% | 0.83% | 2.49% | NA |
| VI/Aromatic | 96 | 4.20% | 8.30% | 0.00% | 85.42% | GTT: 2.08% |
| Intermediate | 90 | 25.60% | 12.20% | 2.22% | 60.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804463121 | GT -> G | LOC_Os08g07900.1 | upstream_gene_variant ; 2899.0bp to feature; MODIFIER | silent_mutation | Average:10.178; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463121 | GT -> G | LOC_Os08g07910.1 | upstream_gene_variant ; 2001.0bp to feature; MODIFIER | silent_mutation | Average:10.178; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463121 | GT -> G | LOC_Os08g07930.1 | upstream_gene_variant ; 2907.0bp to feature; MODIFIER | silent_mutation | Average:10.178; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463121 | GT -> G | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.178; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463121 | GT -> DEL | N | N | silent_mutation | Average:10.178; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463121 | GT -> GTT | LOC_Os08g07900.1 | upstream_gene_variant ; 2900.0bp to feature; MODIFIER | silent_mutation | Average:10.178; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463121 | GT -> GTT | LOC_Os08g07910.1 | upstream_gene_variant ; 2002.0bp to feature; MODIFIER | silent_mutation | Average:10.178; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463121 | GT -> GTT | LOC_Os08g07930.1 | upstream_gene_variant ; 2906.0bp to feature; MODIFIER | silent_mutation | Average:10.178; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463121 | GT -> GTT | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.178; most accessible tissue: Callus, score: 47.315 | N | N | N | N |