| Variant ID: vg0804463132 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 4463132 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGTATTTGATCCTAGATAGATATAGCAGATGCTTACATGGTCTAAGTAACATTCTTTGATAAGGTTTAATGCATATAAATATTGCATCAGTTTTTTTTTA[A/T]
AAAAAAAATTCTTCAATTGTTGTGATATATGCGCCCCAACCGATTTGAACTCTCAATGTAGGACTAATATATTCCCGGGTATTATGTTCACCTCCATTAA
TTAATGGAGGTGAACATAATACCCGGGAATATATTAGTCCTACATTGAGAGTTCAAATCGGTTGGGGCGCATATATCACAACAATTGAAGAATTTTTTTT[T/A]
TAAAAAAAAACTGATGCAATATTTATATGCATTAAACCTTATCAAAGAATGTTACTTAGACCATGTAAGCATCTGCTATATCTATCTAGGATCAAATACG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.40% | 0.30% | 1.08% | 64.18% | NA |
| All Indica | 2759 | 4.70% | 0.50% | 0.65% | 94.09% | NA |
| All Japonica | 1512 | 95.00% | 0.00% | 0.20% | 4.76% | NA |
| Aus | 269 | 3.30% | 0.00% | 6.69% | 89.96% | NA |
| Indica I | 595 | 7.90% | 0.00% | 0.67% | 91.43% | NA |
| Indica II | 465 | 7.50% | 0.20% | 0.43% | 91.83% | NA |
| Indica III | 913 | 0.50% | 0.80% | 0.77% | 97.92% | NA |
| Indica Intermediate | 786 | 5.60% | 0.80% | 0.64% | 93.00% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.13% | 1.43% | NA |
| Tropical Japonica | 504 | 88.70% | 0.00% | 0.20% | 11.11% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.41% | 2.07% | NA |
| VI/Aromatic | 96 | 13.50% | 1.00% | 9.38% | 76.04% | NA |
| Intermediate | 90 | 41.10% | 0.00% | 3.33% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804463132 | A -> T | LOC_Os08g07900.1 | upstream_gene_variant ; 2909.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463132 | A -> T | LOC_Os08g07910.1 | upstream_gene_variant ; 2011.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463132 | A -> T | LOC_Os08g07930.1 | upstream_gene_variant ; 2897.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463132 | A -> T | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463132 | A -> DEL | N | N | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |