| Variant ID: vg0108457644 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 8457644 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 268. )
CCCCTACGGTGTCTCCGGATACCGTCAGGAGATACGAAAGCGCTATCTCTGATCTCGCCGGGCACAGATTCGAGGAGGAAGACTACCCTGTTGTCGACTA[C/T]
GAGTCAGACCTTCAGACCGACATGTCCACAACAGTTAGATAGGCTACCCACATATTGTACTGGTGTGATTATGGTGAATAAAAGCAATACCGGCTTCGGC
GCCGAAGCCGGTATTGCTTTTATTCACCATAATCACACCAGTACAATATGTGGGTAGCCTATCTAACTGTTGTGGACATGTCGGTCTGAAGGTCTGACTC[G/A]
TAGTCGACAACAGGGTAGTCTTCCTCCTCGAATCTGTGCCCGGCGAGATCAGAGATAGCGCTTTCGTATCTCCTGACGGTATCCGGAGACACCGTAGGGG
| 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 | 97.80% | 0.00% | 1.61% | 0.59% | NA |
| All Indica | 2759 | 96.90% | 0.00% | 2.32% | 0.76% | NA |
| All Japonica | 1512 | 99.10% | 0.00% | 0.46% | 0.46% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 98.70% | 0.00% | 1.34% | 0.00% | NA |
| Indica II | 465 | 88.20% | 0.00% | 9.03% | 2.80% | NA |
| Indica III | 913 | 99.30% | 0.00% | 0.22% | 0.44% | NA |
| Indica Intermediate | 786 | 98.00% | 0.00% | 1.53% | 0.51% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.26% | 0.26% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.00% | 1.66% | 2.07% | NA |
| VI/Aromatic | 96 | 95.80% | 1.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0108457644 | C -> T | LOC_Os01g15070.1 | synonymous_variant ; p.Tyr73Tyr; LOW | synonymous_codon | Average:53.831; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |
| vg0108457644 | C -> DEL | LOC_Os01g15070.1 | N | frameshift_variant | Average:53.831; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |