| Variant ID: vg0503844375 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 3844375 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGGGCCAACTAGTTAATTAATGTGTTTCACCATCACATTATAGATTTCATAAGAGATGTACTAGGATTGTGGGAGTACTTCTCAATTTCGTTTTTTTTTA[A/T]
AAAAAATGCACTTTTGAACATTAACTGTTGTCTTGAGCATAAACATGCAAAATGTGTATAACCAAGAATATATGATCTTCCTAGTAATGGTGCTCAAAAG
CTTTTGAGCACCATTACTAGGAAGATCATATATTCTTGGTTATACACATTTTGCATGTTTATGCTCAAGACAACAGTTAATGTTCAAAAGTGCATTTTTT[T/A]
TAAAAAAAAACGAAATTGAGAAGTACTCCCACAATCCTAGTACATCTCTTATGAAATCTATAATGTGATGGTGAAACACATTAATTAACTAGTTGGCCCT
| 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 | 48.30% | 0.30% | 2.09% | 49.32% | NA |
| All Indica | 2759 | 17.80% | 0.00% | 0.80% | 81.41% | NA |
| All Japonica | 1512 | 98.50% | 0.00% | 0.26% | 1.19% | NA |
| Aus | 269 | 85.10% | 4.50% | 0.00% | 10.41% | NA |
| Indica I | 595 | 6.70% | 0.00% | 0.67% | 92.61% | NA |
| Indica II | 465 | 25.80% | 0.00% | 1.08% | 73.12% | NA |
| Indica III | 913 | 14.70% | 0.00% | 0.55% | 84.78% | NA |
| Indica Intermediate | 786 | 24.90% | 0.10% | 1.02% | 73.92% | NA |
| Temperate Japonica | 767 | 98.20% | 0.00% | 0.13% | 1.69% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 1.24% | 1.24% | NA |
| VI/Aromatic | 96 | 15.60% | 1.00% | 73.96% | 9.38% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 2.22% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0503844375 | A -> T | LOC_Os05g07260.1 | downstream_gene_variant ; 1206.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844375 | A -> T | LOC_Os05g07260.2 | downstream_gene_variant ; 1217.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844375 | A -> T | LOC_Os05g07260.4 | downstream_gene_variant ; 1217.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844375 | A -> T | LOC_Os05g07260.3 | downstream_gene_variant ; 1206.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844375 | A -> T | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844375 | A -> DEL | N | N | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |