| Variant ID: vg0700383094 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 383094 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGATCCTATTAAACCTTGTCATAAACATTACTAGTAAATTATATCTATAAACACAAAGCACCTGTCGGTTCGTGGTGACGGAGGTTTTTTTTTCTTTTTC[T/C]
TGGTTACAATCTTTCATGGTGCAAGCCAAATAATTTTTTCCTATTCTATCCAATAAATTATCGCGTTGTCTGGTGCTGATCGTAAAAAAAAAGCATAAAC
GTTTATGCTTTTTTTTTACGATCAGCACCAGACAACGCGATAATTTATTGGATAGAATAGGAAAAAATTATTTGGCTTGCACCATGAAAGATTGTAACCA[A/G]
GAAAAAGAAAAAAAAACCTCCGTCACCACGAACCGACAGGTGCTTTGTGTTTATAGATATAATTTACTAGTAATGTTTATGACAAGGTTTAATAGGATCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.90% | 11.90% | 2.98% | 12.19% | NA |
| All Indica | 2759 | 77.90% | 0.70% | 0.87% | 20.55% | NA |
| All Japonica | 1512 | 57.30% | 35.10% | 7.47% | 0.13% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 44.50% | 1.70% | 0.84% | 52.94% | NA |
| Indica II | 465 | 96.30% | 0.90% | 2.15% | 0.65% | NA |
| Indica III | 913 | 84.00% | 0.20% | 0.22% | 15.55% | NA |
| Indica Intermediate | 786 | 85.10% | 0.40% | 0.89% | 13.61% | NA |
| Temperate Japonica | 767 | 28.00% | 61.10% | 10.82% | 0.00% | NA |
| Tropical Japonica | 504 | 93.30% | 4.20% | 2.18% | 0.40% | NA |
| Japonica Intermediate | 241 | 75.50% | 16.60% | 7.88% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 1.00% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 78.90% | 14.40% | 2.22% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0700383094 | T -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0700383094 | T -> C | LOC_Os07g01610.1 | upstream_gene_variant ; 4778.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0700383094 | T -> C | LOC_Os07g01620.1 | upstream_gene_variant ; 432.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0700383094 | T -> C | LOC_Os07g01640.1 | upstream_gene_variant ; 4866.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0700383094 | T -> C | LOC_Os07g01610-LOC_Os07g01620 | intergenic_region ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |