| Variant ID: vg0100791192 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 791192 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.65, T: 0.35, others allele: 0.00, population size: 69. )
ATTACTAAACTTTGATGTAAACTATTTTTTTTTCTTCCTTCCTTCAGGTTCACAAGTCATCCTCATTGCAGGTAATGCAGATATTCCCTGTTCTTCAAAT[T/C]
CTCGCCTGTCAGCAACCAAGATTTTGTGTACTCTTGTTCCAATAAGAGTTGCTTTGTTCCTTTTTCTTTTTGTTTCAAAAAGCAGATATTAGCTCACACC
GGTGTGAGCTAATATCTGCTTTTTGAAACAAAAAGAAAAAGGAACAAAGCAACTCTTATTGGAACAAGAGTACACAAAATCTTGGTTGCTGACAGGCGAG[A/G]
ATTTGAAGAACAGGGAATATCTGCATTACCTGCAATGAGGATGACTTGTGAACCTGAAGGAAGGAAGAAAAAAAAATAGTTTACATCAAAGTTTAGTAAT
| 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 | 39.70% | 16.00% | 1.61% | 42.66% | NA |
| All Indica | 2759 | 46.60% | 3.00% | 2.32% | 48.06% | NA |
| All Japonica | 1512 | 29.20% | 43.50% | 0.26% | 26.98% | NA |
| Aus | 269 | 34.90% | 0.40% | 0.37% | 64.31% | NA |
| Indica I | 595 | 68.20% | 0.80% | 0.50% | 30.42% | NA |
| Indica II | 465 | 73.10% | 2.20% | 1.51% | 23.23% | NA |
| Indica III | 913 | 16.60% | 1.30% | 3.07% | 78.97% | NA |
| Indica Intermediate | 786 | 49.20% | 7.30% | 3.31% | 40.20% | NA |
| Temperate Japonica | 767 | 2.70% | 67.40% | 0.39% | 29.47% | NA |
| Tropical Japonica | 504 | 77.60% | 5.40% | 0.00% | 17.06% | NA |
| Japonica Intermediate | 241 | 12.40% | 47.30% | 0.41% | 39.83% | NA |
| VI/Aromatic | 96 | 7.30% | 2.10% | 2.08% | 88.54% | NA |
| Intermediate | 90 | 53.30% | 14.40% | 5.56% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100791192 | T -> DEL | N | N | silent_mutation | Average:36.057; most accessible tissue: Callus, score: 66.916 | N | N | N | N |
| vg0100791192 | T -> C | LOC_Os01g02430.1 | upstream_gene_variant ; 2573.0bp to feature; MODIFIER | silent_mutation | Average:36.057; most accessible tissue: Callus, score: 66.916 | N | N | N | N |
| vg0100791192 | T -> C | LOC_Os01g02460.1 | upstream_gene_variant ; 3307.0bp to feature; MODIFIER | silent_mutation | Average:36.057; most accessible tissue: Callus, score: 66.916 | N | N | N | N |
| vg0100791192 | T -> C | LOC_Os01g02450.1 | downstream_gene_variant ; 1896.0bp to feature; MODIFIER | silent_mutation | Average:36.057; most accessible tissue: Callus, score: 66.916 | N | N | N | N |
| vg0100791192 | T -> C | LOC_Os01g02440.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.057; most accessible tissue: Callus, score: 66.916 | N | N | N | N |