| Variant ID: vg1223000001 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 23000001 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AAACTTTGTAACATTATCCATATTCATATATATATTAATGAATCTTTTTTTAGATAATATATGTTAATAAATATAGACACACACATATATATATATACAT[A/G]
TATATATATATACATATATATATATATTATATATATATATATATAATATATATATATATATGTATGTGTGTGTTTAGATTTATTAACATCTATATAAATG
CATTTATATAGATGTTAATAAATCTAAACACACACATACATATATATATATATATTATATATATATATATATAATATATATATATATGTATATATATATA[T/C]
ATGTATATATATATATGTGTGTGTCTATATTTATTAACATATATTATCTAAAAAAAGATTCATTAATATATATATGAATATGGATAATGTTACAAAGTTT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 1.00% | 0.30% | 16.50% | 82.20% | NA |
| All Indica | 2759 | 0.70% | 0.60% | 12.69% | 86.05% | NA |
| All Japonica | 1512 | 1.10% | 0.00% | 20.44% | 78.44% | NA |
| Aus | 269 | 2.60% | 0.00% | 29.37% | 68.03% | NA |
| Indica I | 595 | 0.30% | 0.00% | 6.05% | 93.61% | NA |
| Indica II | 465 | 0.90% | 0.00% | 22.15% | 76.99% | NA |
| Indica III | 913 | 0.80% | 1.20% | 12.38% | 85.65% | NA |
| Indica Intermediate | 786 | 0.80% | 0.60% | 12.47% | 86.13% | NA |
| Temperate Japonica | 767 | 0.50% | 0.00% | 19.82% | 79.66% | NA |
| Tropical Japonica | 504 | 2.00% | 0.00% | 18.25% | 79.76% | NA |
| Japonica Intermediate | 241 | 1.20% | 0.00% | 26.97% | 71.78% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 23.96% | 75.00% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 21.11% | 77.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1223000001 | A -> DEL | N | N | silent_mutation | Average:42.87; most accessible tissue: Minghui63 root, score: 66.549 | N | N | N | N |
| vg1223000001 | A -> G | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 257.0bp to feature; MODIFIER | silent_mutation | Average:42.87; most accessible tissue: Minghui63 root, score: 66.549 | N | N | N | N |
| vg1223000001 | A -> G | LOC_Os12g37470.1 | upstream_gene_variant ; 1477.0bp to feature; MODIFIER | silent_mutation | Average:42.87; most accessible tissue: Minghui63 root, score: 66.549 | N | N | N | N |
| vg1223000001 | A -> G | LOC_Os12g37490.1 | downstream_gene_variant ; 2210.0bp to feature; MODIFIER | silent_mutation | Average:42.87; most accessible tissue: Minghui63 root, score: 66.549 | N | N | N | N |